Electronic Submission of a Sequence Listing, a Large Table, or a Computer Program Listing Appendix in Patent Applications, 57035-57058 [2021-22217]

Agencies

• DEPARTMENT OF COMMERCE
• Patent and Trademark Office

[Federal Register Volume 86, Number 196 (Thursday, October 14, 2021)]
[Rules and Regulations]
[Pages 57035-57058]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 2021-22217]


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DEPARTMENT OF COMMERCE

Patent and Trademark Office

37 CFR Part 1

[Docket No. PTO-P-2020-0032]
RIN 0651-AD48


Electronic Submission of a Sequence Listing, a Large Table, or a 
Computer Program Listing Appendix in Patent Applications

AGENCY: United States Patent and Trademark Office, Department of 
Commerce.

ACTION: Final rule.

-----------------------------------------------------------------------

SUMMARY: The United States Patent and Trademark Office (USPTO or 
Office) is amending the rules of practice to permit higher-capacity 
physical media to be submitted to the USPTO. Patent applications for 
certain inventions require significant data in American Standard Code 
for Information Interchange (ASCII) plain text format to be submitted 
to the USPTO in order to determine whether the invention described in 
the patent application is patentable. When submission of such data 
exceeds the USPTO's patent electronic filing system capacity, 
submission of large data submission in ASCII plain text format can be 
made on physical media. To that end, the rules of practice are amended 
to provide applicants with the ability to use physical media larger 
than compact discs (CDs) for submission of data in ASCII plain text 
format, such as an electronic version of amino acid and nucleotide 
sequence information, information compiled in a large table, or

[[Page 57036]]

information related to a computer program listing. Additionally, 
extraction of compressed data files, which had not been permitted in 
the past for certain submissions, will be permitted if the compressed 
data files are compliant with the requirements of the rules. Other 
rules related to certain obsolete and non-secure methods of presenting 
data are eliminated.

DATES: This rule is effective on November 15, 2021.

FOR FURTHER INFORMATION CONTACT: Mary C. Till, Senior Legal Advisor, 
Office of Patent Legal Administration, Office of the Deputy 
Commissioner for Patents, at [email protected]; or Ali Salimi, Senior 
Legal Advisor, Office of Patent Legal Administration, Office of the 
Deputy Commissioner for Patents, at [email protected].

SUPPLEMENTARY INFORMATION:

Background

    In order to permit the submission of large amounts of data in 
patent applications where such a submission exceeds the capacity for 
filing via the USPTO patent electronic filing system, this rulemaking 
expands the types of physical media that can be used for such a 
submission to include read-only optical discs. The volume of 
applications in which such large amounts of data may need to be 
submitted is a small fraction of the total number of applications that 
the USPTO receives every year. Expanding the types of physical media 
that can be used by these applicants achieves the intent with minimal 
changes to the USPTO's processing of such large amounts of data.
    With respect to the submission of data related to biotechnology 
inventions, the rules of practice no longer permit an applicant to rely 
on a previously submitted computer readable form (CRF) of required 
sequence information. The rules thus ensure the robustness of the data 
by requiring the applicant to confirm that the data presented is the 
correct information for the examiner to consider during the examination 
process. Since the rules will also permit an ASCII plain text file 
(.txt) to serve as both the sequence listing itself and the CRF of the 
sequence listing, these changes are expected to have a minimal impact 
on applicants in general.
    The USPTO encourages applicants to file their patent applications 
via its USPTO patent electronic filing system and imposes a surcharge 
for non-electronic filing of an original patent application (excluding 
reissue, design, plant, and provisional applications), as mandated by 
section 10(h) of Public Law 112-29, September 16, 2011 (Leahy-Smith 
America Invents Act). The USPTO provides information (Legal Framework 
for Patent Electronic System) concerning electronic filing via the 
USPTO patent electronic filing system on its website at www.uspto.gov/patents-application-process/filing-online/legal-framework-efs-web and 
in section 502.05 of the Manual of Patent Examining Procedure (MPEP, 
Ninth Edition, Revision 10.2019). In particular, the USPTO patent 
electronic filing system permits submission of ASCII plain text files 
for submission of a ``Sequence Listing,'' a CRF of a ``Sequence 
Listing,'' ``Large Tables,'' and a ``Computer Program Listing 
Appendix.'' Although a USPTO patent electronic filing system submission 
of such ASCII plain text files is preferred, it is possible that the 
system limitations of the USPTO patent electronic filing system may not 
accommodate large ASCII plain text files. The changes to the rules of 
practice pertaining to a ``Sequence Listing,'' a CRF of a ``Sequence 
Listing,'' ``Large Tables,'' and a ``Computer Program Listing 
Appendix'' incorporate the requirements and conditions for such 
submissions set forth in the Legal Framework for Patent Electronic 
System into the rules of practice for filing such documents in 
electronic form and expand the types of physical media acceptable for 
submissions that exceed the USPTO patent electronic filing system 
limits. The changes do not alter the requirements and conditions set 
forth in the Legal Framework for Patent Electronic System.
    Submission of ASCII plain text files: Electronic documents in ASCII 
file format that are to become part of the permanent USPTO records in 
the file of a patent application, reexamination, or supplemental 
examination proceeding that exceed the USPTO patent electronic filing 
system limits may be submitted on a compact disc. However, due to the 
limited storage capacity of compact discs, the USPTO is revising the 
rules to permit the use of Digital Video Disc-Recordable (DVD-R or 
DVD+R) as an alternative to a compact disc. These higher-capacity read-
only optical discs, on which data is permanently recorded and cannot be 
changed or erased, significantly reduce the number of physical media 
required to accommodate large files.
    In the case of a ``Sequence Listing,'' MPEP section 2422.03 
indicates that if a new application is filed via the USPTO patent 
electronic filing system with an ASCII plain text file of a ``Sequence 
Listing'' that complies with the requirements of 37 CFR 1.824(a)(2) 
through (6) and (b), and if the applicant has not filed a ``Sequence 
Listing'' in a Portable Document Format (PDF) image file, the text file 
will serve as both the paper copy required by 37 CFR 1.821(c) and the 
CRF required by 37 CFR 1.821(e). This procedure is expressly 
incorporated into these changes to the rules of practice. The current 
size limitation for an ASCII plain text file of a ``Sequence Listing'' 
submitted via the USPTO patent electronic filing system is 100 
megabytes (MB). Thus, if an applicant files an ASCII plain text file of 
a ``Sequence Listing'' that is 100 MB or less, that ASCII plain text 
file serves as both the ``Sequence Listing'' under 37 CFR 1.821(c) and 
the CRF of the ``Sequence Listing'' under 37 CFR 1.821(e). With respect 
to ``Large Tables'' and a ``Computer Program Listing Appendix,'' if 
ASCII plain text files are filed through the USPTO patent electronic 
filing system, then no separate submission of disc copies of ASCII 
plain text files are needed. However, the current system limit on ASCII 
plain text file submissions of ``Large Tables'' and a ``Computer 
Program Listing Appendix'' is 25 MB per submission. This limit, 
however, may not prevent an entirely electronic submission. According 
to the Legal Framework for Patent Electronic System, cited supra, a 
user may be able to break up a ``Computer Program Listing Appendix'' or 
``Large Tables'' file that is larger than 25 MB into multiple files 
that are no larger than 25 MB each and submit those smaller files via 
the USPTO patent electronic filing system. If the user chooses to break 
up a large ``Computer Program Listing Appendix'' or ``Large Tables'' 
file so it may be submitted electronically, the file names must 
indicate their order (e.g., ``1 of X,'' ``2 of X''). Files above the 25 
MB limit for ``Large Tables'' and a ``Computer Program Listing 
Appendix'' (unless capable of being divided) and above 100 MB for a 
``Sequence Listing'' must be submitted on read-only optical discs. 
Submission of a ``Sequence Listing'' as an ASCII plain text file, if it 
exceeds 100 MB, cannot be divided like a submission of a ``Large 
Table'' or a ``Computer Program Listing Appendix.'' Thus, any 
``Sequence Listing'' greater than 100 MB must be submitted on read-only 
optical discs. Prior to this rulemaking, such files could not be 
compressed; thus, necessitating the use of multiple CD-ROMs or CD-Rs. 
The changes to the rules of practice will permit higher-capacity media 
as well as non-self-extracting file compression. By permitting file 
compression, material submitted on a read-only optical disc

[[Page 57037]]

can fit on a single disc with the data integrity remaining intact.
    Prior to this rulemaking, the rules of practice (37 CFR 1.52(e), 
1.96(c), and 1.824) recited the use of certain obsolete computer and 
operating system formats. Updated computer and operating system formats 
are now added, and references to obsolete media are eliminated. Changes 
to 37 CFR 1.58 recite the updated computer and operating system 
compatibilities.
    When a patent application relies on subject matter from an ASCII 
plain text file submitted on physical media or via the USPTO patent 
electronic filing system, the patent specification must contain an 
incorporation by reference statement pursuant to 37 CFR 1.77(b)(5) or 
the Legal Framework for Patent Electronic System. The rules related to 
the arrangement of the specification clarify the required incorporation 
by reference statement. The granted patent or pre-grant publication of 
an application that includes an ASCII plain text file, whether 
submitted on optical read-only discs or via the USPTO patent electronic 
filing system, may not include the actual contents of the ASCII plain 
text file in the printed document. The incorporation by reference is 
necessary to treat the material in the ASCII plain text file as part of 
the patent or publication and to alert the public that the granted 
patent or the pre-grant publication includes additional material that 
constitutes part of the patent or publication. Although the present 
changes to the rules of practice permit a cross-reference to related 
applications to be included in the specification, in accordance with 37 
CFR 1.76, it should be noted that the USPTO does not recognize a 
benefit or priority claim presented only in the specification for 
patent applications filed on or after September 16, 2012. For these 
applications or patents issued from such applications, a benefit claim 
(37 CFR 1.78) or priority claim (37 CFR 1.55) must be presented on an 
Application Data Sheet for an original application in order to be 
recognized by the USPTO.
    Submission of data related to disclosures of amino acids and/or 
nucleotides: Any patent application that contains unbranched nucleotide 
sequences with 10 or more nucleotide bases or unbranched, non-D amino 
acid sequences with 4 or more amino acids, provided that there are at 
least 10 ``specifically defined'' nucleotides or 4 ``specifically 
defined'' amino acids, must contain a submission of such data referred 
to as a ``Sequence Listing'' and a CRF of the ``Sequence Listing.'' 
Prior to this rulemaking, a ``Sequence Listing'' exceeding the USPTO 
patent electronic filing system submission limit had to be submitted 
with a total of three disc copies to the USPTO to comply with the 
``Sequence Listing'' regulation requirements. The three disc copies 
included (1) a first disc copy of the ASCII plain text file on a 
compact disc to comply with 37 CFR 1.821(c), (2) a second identical 
disc copy of the ASCII plain text file on compact disc to comply with 
the duplicate submission requirement in 37 CFR 1.52(e)(4) when 
submitting the 37 CFR 1.821(c) sequence listing, and (3) a CRF copy of 
the ASCII plain text file on compact disc, identical to the 37 CFR 
1.821(c) submission. The present rule changes permit that a single 
read-only optical disc copy of a ``Sequence Listing'' as an ASCII plain 
text file can be submitted, and that such submission will comply with 
both the listing requirement (37 CFR 1.821(c)) and the CRF requirement 
(37 CFR 1.821(e)). For submission via the USPTO patent electronic 
filing system, the ASCII plain text file, not the PDF version, will 
serve to comply with both 37 CFR 1.821(c) and 1.821(e). The following 
table summarizes the mechanics of submitting a ``Sequence Listing'' 
under the changes to the rules of practice in applications, except for 
international applications during the international stage, based on the 
current USPTO patent electronic filing system limit of 100 MB for an 
ASCII plain text file and a system limit of 25 MB for PDF files.

----------------------------------------------------------------------------------------------------------------
                                                                                                Surcharge under
                                                                                              37 CFR 1.21(o) for
                                     Preferred            Acceptable         Specification      submission of a
 Size of  ``Sequence Listing''       submission           submission           statement          ``Sequence
                                                                             requirements        Listing'' in
                                                                                                electronic form
----------------------------------------------------------------------------------------------------------------
100 MB or less................  ASCII plain text     The ``Sequence       Incorporation by    None.
                                 file submitted via   Listing'' in         reference of the
                                 the USPTO patent     physical paper       ASCII plain text
                                 electronic filing    copies or            file into the
                                 system, complies     submitted via the    specification
                                 with both 37 CFR     USPTO patent         (see MPEP 502.05).
                                 1.821(c) and         electronic filing
                                 1.821(e), no         system as a PDF
                                 separate CRF         image file and a
                                 needed.              CRF on a read-only
                                                      optical disc along
                                                      with a statement
                                                      that the CRF and
                                                      the physical paper/
                                                      PDF image file
                                                      submission are the
                                                      same.
101 MB to 299 MB..............  ASCII plain text     The ``Sequence       Incorporation by    None.
                                 file submitted on    Listing'' in         reference of the
                                 a read-only          physical paper       ASCII plain text
                                 optical disc in a    copies and a CRF     file into the
                                 single copy, the     on a read-only       specification (37
                                 single copy          optical disc along   CFR 1.52(e)(8) as
                                 complies with both   with a statement     added in these
                                 37 CFR 1.821(c)      that the CRF and     rules).
                                 and 1.821(e), no     the physical paper
                                 separate CRF         submission are the
                                 needed.              same.
300 MB to 799 MB..............  ASCII plain text     The ``Sequence       Incorporation by    37 CFR 1.21(o)(1):
                                 file submitted on    Listing'' in         reference of the    Currently $1,060
                                 a read-only          physical paper       ASCII plain text    for an
                                 optical disc in a    copies and a CRF     file into the       undiscounted
                                 single copy, the     on a read-only       specification (37   entity, $530 for
                                 single copy          optical disc along   CFR 1.52(e)(8) as   a small entity,
                                 complies with both   with a statement     added in these      and $265 for a
                                 37 CFR 1.821(c)      that the CRF and     rules).             micro entity.
                                 and 1.821(e), no     the physical paper
                                 separate CRF         submission are the
                                 needed.              same.

[[Page 57038]]

 
800 MB or above...............  ASCII plain text     The ``Sequence       Incorporation by    37 CFR 1.21(o)(2):
                                 file submitted on    Listing'' in         reference of the    Currently $10,500
                                 a read-only          physical paper       ASCII plain text    for an
                                 optical disc in a    copies and a CRF     file into the       undiscounted
                                 single copy, the     on a read-only       specification (37   entity, $5,250
                                 single copy          optical disc along   CFR 1.52(e)(8) as   for a small
                                 complies with both   with a statement     added in these      entity, and
                                 37 CFR 1.821(c)      that the CRF and     rules).             $2,625 for a
                                 and 1.821(e), no     the physical paper                       micro entity.
                                 separate CRF         submission are the
                                 needed. Should       same.
                                 more than one disc
                                 be needed, then
                                 only a single copy
                                 of the additional
                                 disc(s) would be
                                 needed, no
                                 additional CRF
                                 needed since the
                                 read-only optical
                                 discs (if multiple
                                 are needed) need
                                 NOT be submitted
                                 in duplicate.
----------------------------------------------------------------------------------------------------------------

    Prior to this rulemaking, the rules of practice related to the 
form, content, and submission requirements of ``Sequence Listings'' 
complied with World Intellectual Property Organization (WIPO) Standard 
ST.25. The rule changes and modifications in this document also conform 
to WIPO Standard ST.25.
    To simplify and streamline the processing of patent applications 
with sequences of amino acids and nucleotides, as defined in 37 CFR 
1.821(a), submission of a ``Sequence Listing'' in ASCII plain text file 
format, either directly via the USPTO patent electronic filing system 
or on a read-only optical disc, will be sufficient to comply with the 
listing requirement and the CRF requirement (37 CFR 1.821(c) and 
1.821(e)). That is, if a ``Sequence Listing'' in ASCII plain text file 
format is filed either directly via the USPTO patent electronic filing 
system or on a read-only optical disc, then no additional CRF copy will 
be needed. In such a situation, an incorporation by reference statement 
in the specification, in accordance with 37 CFR 1.77(b)(5), would still 
be required, except such a statement will not be required in an 
international application during the international stage. As with the 
rules prior to this rulemaking, the present changes continue to permit 
the submission of a ``Sequence Listing'' on physical sheets of paper or 
as a PDF image file. Furthermore, like the previous rules, the present 
rules will require payment of the application size fee (37 CFR 1.16(s)) 
for physical sheets of paper of a ``Sequence Listing'' or a PDF of a 
``Sequence Listing'' that results in an application size that exceeds 
100 sheets of paper. Submission of the ``Sequence Listing'' as a PDF or 
on physical sheets of paper will still require a separate CRF of the 
``Sequence Listing.'' Similarly, should the ASCII plain text file of 
the ``Sequence Listing'' exceed the system limits of the USPTO patent 
electronic filing system (currently at 100 MB), then a single copy of 
an ASCII plain text file of the ``Sequence Listing'' submitted on a 
read-only optical disc will not require a separate electronic copy of a 
CRF of the ``Sequence Listing.'' In circumstances in which a separate 
CRF is filed, the statement, in accordance with 37 CFR 1.821(e)(1)(ii) 
and 1.821(e)(2)(ii), that the CRF is identical to either the PDF or the 
physical paper version of the ``Sequence Listing'' is required.
    The rule changes no longer permit the transfer of a CRF from a 
parent or related application to another application. In light of the 
ability to download a ``Sequence Listing'' from granted U.S. patents 
and U.S. patent application publications via Public Patent Application 
Information Retrieval (PAIR) in the Supplemental Content tab, there is 
no longer a need for a CRF transfer. Such electronic copies of a 
``Sequence Listing'' may also be available on another intellectual 
property office's website or on the WIPO--PATENTSCOPE website. In the 
extremely rare circumstance in which the ``Sequence Listing'' exceeds 
the download capability (currently 650 MB), then a request for the 
content of a granted U.S. patent or U.S. patent application publication 
(including the ``Sequence Listing'' submitted on disc) can be made to 
the Patent and Trademark Copy Fulfillment Branch. Therefore, these 
changes to the rules of practice eliminate the practice of CRF 
transfers.
    As noted earlier, the present changes will continue to permit the 
submission of a ``Sequence Listing'' on physical sheets of paper or as 
a PDF image file. However, WIPO Standard ST.26 is currently scheduled 
to take effect on January 1, 2022, and will replace WIPO Standard 
ST.25. WIPO Standard ST.26 will require that a ``Sequence Listing'' 
must be presented as a single file in eXtensible Markup Language (XML). 
Presentation in XML file format cannot be accomplished on paper or as a 
PDF image file. As a result, in an original application filed on or 
after WIPO Standard ST.26 takes effect (currently scheduled to happen 
on January 1, 2022), the ``Sequence Listing'' part will not be accepted 
on physical sheets of paper or as a PDF image file. To prepare for the 
changes under WIPO Standard ST.26, the USPTO is revising the rules of 
practice to facilitate ``Sequence Listing'' submissions by permitting a 
single ASCII plain text file submission to both meet the ``Sequence 
Listing'' requirement and serve as the CRF of the ``Sequence Listing.'' 
That is, under these rule changes, a single ASCII plain text file 
submission of a ``Sequence Listing'' will comply with both 37 CFR 
1.821(c) and (e).
    Prior to this rulemaking, 37 CFR 1.821(a) incorporated by reference 
six tables from Appendix 2 of WIPO Standard ST.25 that provide the 
nucleotide and amino acid symbols and feature tables. For convenience, 
the present rulemaking adds these tables as Appendices A-F of subpart G 
of part 1 (explicitly incorporating the text of the WIPO tables into 
the CFR). Prior to this rulemaking, 37 CFR 1.823(b) also included a 
table containing all numeric identifiers. To improve the readability of 
the regulations, this table is moved to Appendix G.
    Updates to amendment practice for ``Large Tables,'' a ``Computer 
Program Listing Appendix,'' and ``Sequence Listings'': In general, the 
manner of making amendments in applications requires that the text of 
any added subject matter must be shown by underlining the added text 
and that the text of any deleted matter must be shown by strike-
through. However, computer listings (37 CFR 1.96) and ``Sequence 
Listings'' (37 CFR 1.825)

[[Page 57039]]

were exempted from these general requirements (37 CFR 1.121(b)) prior 
to this rulemaking. The present changes to the rules of practice will 
require a description of the amendments made in ``Large Tables,'' a 
``Computer Program Listing Appendix,'' and ``Sequence Listings'' to 
more easily and accurately identify any changes made to the information 
contained in such submissions (37 CFR 1.121(b)(6)).
    This rule includes requirements for amendments to an ASCII plain 
text file containing ``Large Tables'' (37 CFR 1.58(g)) or a ``Computer 
Program Listing Appendix'' (37 CFR 1.96(c)(5)(i)) that are accomplished 
by a replacement of the ASCII plain text file. Providing a replacement 
may be required if, for example, the information on the disc is 
corrupted. A replacement ASCII plain text file must be submitted, 
either via the USPTO patent electronic filing system or on a read-only 
optical disc, together with an incorporation by reference of the 
material in the replacement ASCII plain text file in a separate 
paragraph of the specification; a statement that identifies the 
location of all deletions, replacements, or additions to the ASCII 
plain text file; and a statement that the replacement ASCII plain text 
file contains no new matter.

Discussion of Specific Rules

    The following is a discussion of the amendments to 37 CFR part 1.

Section 1.52

    The heading of Sec.  1.52 is revised to read: Language, paper, 
writing, margins, read-only optical disc specifications.
    Section 1.52(e) is amended to reference electronic documents 
``submitted on a read-only optical disc,'' with additional conforming 
changes made throughout. Since Sec.  1.52(e) only governs electronic 
documents submitted on discs, in particular, read-only optical discs, 
the heading is more specific to the types of electronic documents 
covered by the regulation.
    Section 1.52(e)(1) is updated to specifically refer to a ``Computer 
Program Listing Appendix,'' as provided for in Sec.  1.96(c), and to 
require that the ``Sequence Listing'' on a read-only optical disc 
submitted under Sec.  1.821(c) must be in compliance with Sec.  1.824. 
Section 1.52(e)(1) is revised to indicate that ``Large Tables,'' as 
described in Sec.  1.58(c), may be submitted on a read-only optical 
disc to become part of the permanent USPTO record.
    Section 1.52(e)(2) is revised to replace ``compact'' with ``read-
only optical'' and to incorporate conformity to the International 
Organization for Standardization (ISO) 9660 standard, which was 
previously located in Sec.  1.52(e)(3). Additionally, Sec.  1.52(e)(2) 
maintains the availability of CD-ROM and CD-R as options for physical 
media (Sec.  1.52(e)(2)(i)) but also expands the types of media options 
to include DVD-R or DVD+R (Sec.  1.52(e)(2)(ii)).
    Section 1.52(e)(3) is reorganized for improved readability. The 
computer compatibility (Sec.  1.52(e)(3)(i)) and operating system 
compatibility (Sec.  1.52(e)(3)(ii)) are expressly provided. 
Furthermore, the changes to the rules of practice indicate that the use 
of ASCII plain text is required when submitting files on physical media 
(Sec.  1.52(e)(3)(iii)). The changes permit file compression for ASCII 
plain text files, which must be done in accordance with Sec. Sec.  
1.58, 1.96, and 1.824, as applicable (Sec.  1.52(e)(3)(iii)).
    Section 1.52(e)(4) is revised to eliminate its requirements for a 
duplicate copy and accompanying statement that the two discs are 
identical. References to ``Copy 1'' and ``Copy 2'' are deleted, and 
references to ``compact disc'' are updated to ``read-only optical 
disc.'' However, duplicate copies of read-only optical discs for 
``Large Tables'' or a ``Computer Program Listing Appendix'' will still 
be required, and Sec. Sec.  1.58 and 1.96 are amended to provide for 
such duplicate copies. Duplicate copies for ``Large Tables'' and a 
``Computer Program Listing Appendix'' will still be required to be 
submitted since the Office of Patent Application Processing (OPAP) 
keeps a first copy for record retention purposes and a second copy in 
an artifact folder for use by the examiner during the patent 
examination process. A ``Sequence Listing,'' however, is not processed 
in the same manner. Accordingly, only a single copy of a read-only 
optical disc containing the ``Sequence Listing'' in ASCII plain text is 
needed, as such copy will serve as both the listing, as required by 37 
CFR 1.821(c), and the CRF copy, as required by 37 CFR 1.821(e). Section 
1.52(e)(4) is also revised to require that the read-only optical discs 
are enclosed in a hard case within an unsealed, padded, and protective 
mailing envelope and that such submission is accompanied by a 
transmittal letter. The information regarding the read-only optical 
disc to be included in the transmittal letter is expressly enumerated 
in items (i)-(vi) of this rule.
    Section 1.52(e)(5) is revised to enumerate the labeling 
requirements for the read-only optical disc that had previously been 
enumerated in Sec.  1.52(e)(6). The incorporation by reference found in 
the current Sec.  1.52(e)(5) is deleted and moved to Sec.  1.52(e)(8).
    Section 1.52(e)(6) is revised to state that the read-only optical 
discs may not be retained as part of the patent application file and 
will not be returned to the applicant. The current USPTO processing of 
compact discs will equally apply to read-only optical discs. For 
``Large Tables'' or a ``Computer Program Listing Appendix,'' the 
process involves the OPAP receiving the read-only optical discs, 
creating an artifact sheet for inclusion in the Office file wrapper, 
and reviewing the ASCII plain text file. A first copy of the read-only 
optical disc is kept for record retention purposes, and a second copy 
is maintained in an artifact folder for use by the examiner during the 
patent examination process. For a ``Sequence Listing,'' the present 
rule change requires the submission of a single read-only optical disc. 
Once the ``Sequence Listing'' is loaded into the USPTO's Supplemental 
Complex Repository for Examiners system, the physical media may be 
retained by the Patent Legal Research Center. A ``Sequence Listing'' 
from granted U.S. patents and U.S. patent application publications is 
available via Public PAIR in the Supplemental Content tab. Such 
electronic copies of a ``Sequence Listing'' may also be available on 
another intellectual property office's website or on the WIPO--
PATENTSCOPE website. In the extremely rare circumstance in which the 
``Sequence Listing'' exceeds the download capability (currently 650 
MB), then a request for the content of a granted U.S. patent or U.S. 
patent application publication (including the ``Sequence Listing'' 
submitted on disc) can be made to the Patent and Trademark Copy 
Fulfillment Branch.
    Section 1.52(e)(7) is revised to state that any amendment to the 
information on a read-only optical disc must be made in accordance with 
specified provisions, in compliance with Sec.  1.58(g) for ``Large 
Tables,'' Sec.  1.96(c)(5) for a ``Computer Program Listing Appendix,'' 
and Sec.  1.825(b) for a ``Sequence Listing'' or a CRF of a ``Sequence 
Listing.''
    Section 1.52(e)(8) is added to state that the specification must 
contain an incorporation by reference (Sec.  1.77(b)(5)) of the 
material contained on each read-only optical disc in a separate 
paragraph, except for an international application in the international 
stage. Additionally, the USPTO may require the applicant to amend the 
specification to include the material incorporated by reference.
    Section 1.52(e)(9) is added to indicate that should a file be 
unreadable, then the USPTO will treat the submission as

[[Page 57040]]

not ever having been submitted. A file is unreadable if, for example, 
it is of a format that does not comply with the requirements of Sec.  
1.52(e)(2), it is corrupted, or it is written onto a defective read-
only optical disc. In such a case, the OPAP will issue a notice 
indicating that the file is unreadable, and a replacement will be 
required.
    Section 1.52(f) is amended to include the subtitle ``Determining 
application size fees for applications containing electronic documents 
submitted on a read-only optical disc or via the USPTO patent 
electronic filing system.''
    Section 1.52(f)(1) is amended to clarify the determination of 
application size fees for application components submitted on a read-
only optical disc in compliance with Sec.  1.52(e), where an electronic 
form of any ``Sequence Listing,'' in compliance with either Sec.  
1.821(c) or (e), and any ``Computer Program Listing Appendix,'' in 
compliance with Sec.  1.96(c), are specifically excluded from the 
application size fee determination. As stated in 35 U.S.C. 41(a)(1)(G), 
``any sequence listing'' or a ``computer program listing'' submitted in 
electronic form is expressly excluded from any application size fee 
calculation. A ``Computer Program Listing Appendix'' is considered a 
``computer program listing.''
    Section 1.52(f)(2) is amended to clarify the determination of 
application size fees for applications submitted in whole or in part 
via the USPTO patent electronic filing system and to also clarify that 
any electronic form of a ``Sequence Listing,'' in compliance with 
either Sec.  1.821(c) or (e), and any ``Computer Program Listing 
Appendix,'' in compliance with Sec.  1.96(c), are specifically excluded 
from the application size fee determination. As stated in 35 U.S.C. 
41(a)(1)(G), ``any sequence listing'' or a ``computer program listing'' 
submitted in electronic form is expressly excluded from any application 
size fee calculation. A ``Computer Program Listing Appendix'' is 
considered a ``computer program listing.''
    Section 1.52(f)(3) is added to provide a cross-reference to 
existing Sec.  1.21(o), which sets forth a surcharge for the submission 
of a ``Sequence Listing'' in electronic form in an application under 35 
U.S.C. 111 or 371 that is 300 MB or larger in size. This means that a 
``Sequence Listing'' submitted in electronic form on read-only optical 
discs, in compliance with either Sec. Sec.  1.821(c) or 1.821(e), that 
is 300 MB or larger in size will incur a surcharge under Sec.  1.21(o). 
When the electronic form of the ``Sequence Listing'' is between 300 MB 
and 800 MB, a surcharge under Sec.  1.21(o)(1) will be required. If the 
electronic form of the ``Sequence Listing'' exceeds 800 MB, a surcharge 
under Sec.  1.21(o)(2) will be imposed.

Section 1.58

    Section 1.58(b) is revised to delete references to Sec. Sec.  
1.96(c) and 1.821(c) regarding tables submitted in electronic form and 
to set forth format requirements, from former Sec.  1.58(c), that apply 
generally to chemical and mathematical formulas and tables.
    Section 1.58(c) is rewritten to define ``Large Tables'' that may be 
submitted in electronic form in ASCII plain text via the USPTO patent 
electronic filing system or on a read-only optical disc, in compliance 
with Sec.  1.52(e), excluding an international application during the 
international stage.
    Section 1.58(d) is added to list the format requirements of ``Large 
Tables'' submitted in electronic form in ASCII plain text. The format 
requirements address the spatial relationship of table elements, 
computer compatibility, operating system compatibility, the use of 
ASCII plain text, the naming conventions for the *.txt file, and an 
incorporation by reference statement to be included in the 
specification, as per Sec.  1.77(b)(5).
    Section 1.58(e) is added to state that ``Large Tables'' submitted 
via the USPTO patent electronic filing system must not exceed 25 MB, 
and file compression is not permitted. It is noted that when submitting 
via the USPTO patent electronic filing system, it is possible to submit 
multiple files that are 25 MB or less in size, as per the Legal 
Framework for Patent Electronic System cited supra.
    Section 1.58(f) is added to specify the technical requirements for 
``Large Tables'' submitted on read-only optical discs, in compliance 
with Sec.  1.52(e), and that compression is permitted. Section 1.58(f) 
also specifies the permitted manner of file compression.
    Section 1.58(g) is added to provide the procedure that will be 
applicable should an amendment of one or more ``Large Tables'' be 
required. If an amendment is required to be made to a ``Large Table,'' 
then a replacement submission via the USPTO patent electronic filing 
system or on duplicate read-only optical discs will be necessary. An 
updated incorporation by reference statement will be required, along 
with the necessary statement regarding any deletions, replacements, or 
additions to the ASCII plain text file. Additionally, a statement that 
the replacement ASCII plain text file contains no new matter will also 
be required.
    Section 1.58(h) is added to specify that should ``Large Tables'' be 
submitted as an ASCII plain text file on the application filing date, 
but no incorporation by reference of the material contained therein has 
been made, an amendment containing a separate paragraph incorporating 
by reference the material contained in the ASCII plain text file, as 
per Sec.  1.77(b)(5), will be required.
    Section 1.58(i) is added to require that any read-only optical disc 
for a ``Large Table'' be submitted in duplicate. Section 1.58(i) sets 
forth the criteria for labeling and necessary statements as to the 
identity of the read-only optical discs. This section indicates how the 
USPTO will treat the submission of the two read-only optical disc 
copies that are not identical to each other. Two discs would be 
considered not identical when, e.g., the files contained on those discs 
are not the same. Duplicate copies for ``Large Tables'' are required to 
be submitted since the OPAP keeps a first copy for record retention 
purposes and a second copy in an artifact folder for use by the 
examiner during the patent examination process.
    Section 1.58(j) is added to require that any amendment to the 
information on a read-only optical disc must be by way of duplicate 
replacement read-only optical discs, in compliance with Sec.  1.58(g), 
where the replacement read-only optical disc and copy must be labeled 
``COPY 1 REPLACEMENT MM/DD/YYYY'' (with the month, day, and year of 
creation indicated) and ``COPY 2 REPLACEMENT MM/DD/YYYY,'' 
respectively. This section indicates how the USPTO will treat the 
submission of the two replacement read-only optical disc copies that 
are not identical to each other. Two discs would be considered not 
identical when, e.g., the files contained on those discs are not the 
same.

Section 1.71

    Section 1.71(f) is revised to clarify that a ``Sequence Listing,'' 
if required or submitted under Sec.  1.821(c), should be submitted on a 
separate sheet. This is directed to those submissions of the ``Sequence 
Listing'' submitted on physical sheets of paper or as a PDF image file 
via the USPTO patent electronic filing system. In such cases where 
there is a ``Sequence Listing'' and a separate CRF of the ``Sequence 
Listing,'' the ``Sequence Listing'' must be on a separate sheet(s).

[[Page 57041]]

Section 1.77

    Section 1.77(b)(5) is revised to clarify when an incorporation by 
reference statement is needed. The rule change allows for incorporation 
by reference of ASCII plain text files submitted via the USPTO patent 
electronic filing system or on one or more read-only optical discs for 
a ``Computer Program Listing Appendix,'' a ``Sequence Listing,'' or 
``Large Tables,'' as provided for in Sec.  1.96(c), Sec.  1.821(c), or 
Sec.  1.58(c), respectively. The incorporation by reference statement 
must identify the names of each ASCII plain text file and specify, if 
applicable, the files contained on each of the read-only optical discs, 
their dates of creation, and the sizes of each ASCII plain text file in 
bytes.
    Section 1.77(b)(13) is revised to clarify that the ``Sequence 
Listing'' required by Sec.  1.821(c), submitted on physical sheets of 
paper or as a PDF image file, should follow the other sections of the 
specification.

Section 1.96

    Section 1.96(a) is revised to replace ``printout'' with 
``document.''
    Section 1.96(c) is revised to set forth the requirements that apply 
to any ``Computer Program Listing Appendix'' that will not be part of 
the printed patent specification. The appendix must be submitted as an 
electronic document in ASCII plain text, whether submitted via the 
USPTO patent electronic filing system or on a read-only optical disc, 
in compliance with Sec.  1.52(e). Requirements for the ``Computer 
Program Listing Appendix'' include that it must be incorporated by 
reference in the specification, as set forth in Sec.  1.77(b)(5), and 
have certain computer compatibilities (Sec.  1.96(c)(1)), naming 
convention adherences (Sec.  1.96(c)(2)), and size limitations (Sec.  
1.96(c)(3)).
    Section 1.96(c)(4) is added to state requirements (i) through (vi), 
where the ``Computer Program Listing Appendix'' is submitted on a read-
only optical disc, in compliance with Sec.  1.52(e).
    Section 1.96(c)(5) is added to state requirements (i) through (iv) 
for amendments to delete, replace, or add to the information in a 
``Computer Program Listing Appendix'' submitted in electronic form in 
ASCII plain text.
    Section 1.96(c)(6) is added to indicate that should a ``Computer 
Program Listing Appendix'' be present on the filing date of the 
application without an express incorporation by reference in the 
specification related to the material contained in the ASCII plain text 
file, in accordance with Sec.  1.77(b)(5), then an amendment to include 
such a paragraph in the specification will be required.
    Section 1.96(c)(7) is added to indicate that a submission of a 
``Computer Program Listing Appendix'' on a read-only optical disc must 
be completed in duplicate, since the processing by the USPTO of a 
``Computer Program Listing Appendix'' submitted on a read-only optical 
disc involves keeping a first copy for record retention purposes and 
using a second copy during the examination process. The new section 
sets forth the criteria for labeling and necessary statements as to the 
identity of the read-only optical discs. This section indicates how the 
USPTO will treat the submission of the two read-only optical disc 
copies should they not be identical. Two discs would be considered not 
identical when, e.g., the files contained on those discs are not the 
same.

Section 1.121

    Section 1.121(b) is revised, and Sec.  1.121(b)(6) is added, to 
clarify that ``Large Tables,'' in accordance with Sec.  1.58(c); a 
``Computer Program Listing Appendix,'' in accordance with Sec.  
1.96(c)(5) and (7); and a ``Sequence Listing'' or CRF, in accordance 
with Sec.  1.825, must be amended in accordance with Sec.  1.58(g), 
Sec.  1.96(c)(5), and Sec.  1.825, respectively.

Section 1.173

    The heading of Sec.  1.173(b)(1) is revised to reflect that, in a 
reissue application, changes to the claims, ``Large Tables'' (Sec.  
1.58(c)), a ``Computer Program Listing Appendix'' (Sec.  1.96(c)), or a 
``Sequence Listing'' (Sec.  1.821(c)) are made in a different manner 
than changes to other parts of the specification.
    The manner of making changes to the specification, other than to 
the claims, set forth in current Sec.  1.173(b)(1), is moved to new 
Sec.  1.173(b)(1)(i). New Sec.  1.173(b)(1)(i) specifies that it does 
not apply to changes to ``Large Tables'' (Sec.  1.58(c)), a ``Computer 
Program Listing Appendix'' (Sec.  1.96(c)), or a ``Sequence Listing'' 
(Sec.  1.821(c)), in addition to not applying to changes to the claims. 
Additionally, the language from the current Sec.  1.173(b)(1) stating 
that the paragraph is not applicable to discs is not included in the 
new Sec.  1.173(b)(1)(i).
    Section 1.173(b)(1)(ii) is added to specify that changes to ``Large 
Tables,'' a ``Computer Program Listing Appendix,'' or a ``Sequence 
Listing'' must be made in accordance with Sec.  1.58(g) for ``Large 
Tables,'' Sec.  1.96(c)(5) for a ``Computer Program Listing Appendix,'' 
and Sec.  1.825 for a ``Sequence Listing.''
    Section 1.173(d) is revised to exclude changes to ``Large Tables,'' 
a ``Computer Program Listing Appendix,'' or a ``Sequence Listing'' from 
the changes that must be shown by markings in a reissue application.
    Section Sec.  1.173(d)(2) is revised to delete the following: 
``except for amendments submitted on compact discs (Sec. Sec.  1.96 and 
1.821(c)). Matter added by reissue on compact discs must be preceded 
with `U' and end with `U' to properly identify the material being 
added.''

Section 1.530

    The heading of Sec.  1.530(d)(1) is revised to reflect that, in a 
reexamination proceeding, changes to the claims, ``Large Tables'' 
(Sec.  1.58(c)), a ``Computer Program Listing Appendix'' (Sec.  
1.96(c)), and a ``Sequence Listing'' (Sec.  1.821(c)) are made in a 
different manner than changes to the other parts of the specification.
    The manner of making changes to the specification, other than to 
the claims, is moved from Sec.  1.530(d)(1) to new Sec.  
1.530(d)(1)(i). New Sec.  1.530(d)(1)(i) specifies that it does not 
apply to changes to ``Large Tables'' (Sec.  1.58(c)), a ``Computer 
Program Listing Appendix'' (Sec.  1.96(c)), and a ``Sequence Listing'' 
(Sec.  1.821(c)), in addition to not applying to changes to the claims.
    Section 1.530(d)(1)(ii) is added to specify that changes to ``Large 
Tables,'' a ``Computer Program Listing Appendix,'' or a ``Sequence 
Listing'' must be made in accordance with Sec.  1.58(g) for ``Large 
Tables,'' Sec.  1.96(c)(5) for a ``Computer Program Listing Appendix,'' 
and Sec.  1.825 for a ``Sequence Listing.''

Section 1.821

    Section 1.821(a) is revised to remove all prior references to WIPO 
Standard ST.25 (1998) and instead cross-reference new Appendices A 
through F to 37 CFR part 1, subpart G, which will contain the updated 
2009 version of the tables from WIPO Standard ST.25.
    Section 1.821(c) is revised to delete references to a paper or 
compact disc copy (Sec.  1.52(e)), delete discussion of sequence 
identifiers, and indicate that the criteria for submission of a 
``Sequence Listing,'' except for national stage entry under Sec.  
1.495(b)(1), is set forth in the new Sec.  1.821(c)(1)-(3). Information 
about sequence identifiers has been moved to Sec.  1.823(a).
    Section 1.821(c)(1) is added to state that the ``Sequence Listing'' 
can be submitted as an ASCII plain text file via the USPTO patent 
electronic filing system or on a read-only optical disc copy, where the 
form and format of the ``Sequence Listing'' conforms to Sec.  1.824 and 
an incorporation by reference statement, as required by Sec.  
1.823(b)(1),

[[Page 57042]]

is provided. Section 1.821(c)(2) is added to permit the submission of a 
``Sequence Listing'' as a PDF file via the USPTO patent electronic 
filing system. Section 1.821(c)(3) is added to permit the submission of 
a ``Sequence Listing'' on physical sheets of paper.
    Section 1.821(d) is revised to add that where a sequence is 
presented in a drawing, reference must be made to the sequence by use 
of a sequence identifier, either in the drawing or in the Brief 
Description of the Drawings, where the correlation between multiple 
sequences in the drawing and their sequence identifiers in the Brief 
Description is clear. A sequence found in a drawing sheet is not a 
``Sequence Listing'' under Sec.  1.821(c) or (e). Therefore, a separate 
``Sequence Listing'' will be required to comply with Sec.  1.821(c). If 
the ``Sequence Listing'' was submitted as a PDF image file via the 
USPTO patent electronic filing system or on physical sheets of paper, a 
separate CRF of the ``Sequence Listing'' will be required to comply 
with Sec.  1.821(e). When providing reference to the sequence in the 
text of the description or claims, the numeric sequence identifier is 
preceded by ``SEQ ID NO:'' or the like, even if the actual sequence is 
also embedded in the text of the description or claims of the patent 
application. The use of ``SEQ ID NO:'' is preferred, but including ``or 
the like'' is intended to ensure that a formalities notice is not sent 
when an application uses, for example, ``SEQ NO.'' or ``Seq. Id. No.'' 
or any similar identification for an amino acid or nucleotide sequence 
in the specification or claims where it is clear that a sequence from 
the ``Sequence Listing'' is shown in the description or claims.
    Section 1.821(e)(1) is added to set forth the requirements in Sec.  
1.821(e)(1)(i) for submission of a CRF of the ``Sequence Listing,'' in 
compliance with Sec.  1.824, when a ``Sequence Listing'' was submitted 
as a PDF image file via the USPTO patent electronic filing system or on 
physical sheets of paper for an application filed under 35 U.S.C. 
111(a). The rule (Sec.  1.821(e)(1)(ii)) also indicates that a 
statement is required to confirm that the CRF is identical to the 
``Sequence Listing'' under Sec.  1.821(c), when the ``Sequence 
Listing,'' under Sec.  1.821(c), was submitted on physical sheets of 
paper or as a PDF image file via the USPTO patent electronic filing 
system.
    Section 1.821(e)(2) is added to set forth the requirements where 
the ``Sequence Listing,'' under Sec.  1.821(c), in an application 
submitted under 35 U.S.C. 371, is in a PDF file (Sec.  1.821(c)(2)) or 
on physical sheets of paper (Sec.  1.821(c)(3)), and not also as an 
ASCII plain text file, in compliance with Sec.  1.824 (Sec.  
1.821(c)(1)). In such situations, the following are required: (1) A 
copy of the ``Sequence Listing'' in CRF, in accordance with the 
requirements of Sec.  1.824 (Sec.  1.821(e)(2)(i)); and (2) a statement 
that the sequence information contained in the CRF, submitted under 
Sec.  1.821(e)(2)(i), is identical to the sequence information 
contained in the ``Sequence Listing'' submitted as a PDF image file 
(Sec.  1.821(c)(2)) or on physical sheets of paper (Sec.  1.821(c)(3)).
    Section 1.821(e)(3) is added to set forth the requirements where a 
``Sequence Listing'' in ASCII plain text format, in compliance with 
Sec.  1.824, has not been submitted for an international application 
under the Patent Cooperation Treaty (PCT) and where that application 
contains disclosures of nucleotide and/or amino acid sequences, as 
defined in paragraph (a) of this section, and is to be searched by the 
United States International Searching Authority or examined by the 
United States International Preliminary Examining Authority. In such 
situations, the following are required: (1) A copy of the ``Sequence 
Listing'' in CRF, in accordance with the requirements of Sec.  1.824 
(Sec.  1.821(e)(3)(i)); (2) a late furnishing fee for providing a 
``Sequence Listing'' in response to an invitation, as set forth in 
Sec.  1.445(a)(5) (Sec.  1.821(e)(3)(ii)); and (3) a statement that the 
sequence information contained in the CRF submitted under Sec.  
1.821(e)(3)(i) does not go beyond the disclosure in the international 
application as filed, or a statement that the information recorded in 
the ASCII plain text file submitted under Sec.  1.821(e)(3)(i) is 
identical to the sequence listing contained in the international 
application as filed, as applicable (Sec.  1.821(e)(3)(iii)).
    Section 1.821(e)(4) is added to state that the CRF may not be 
retained as a part of the patent application file.
    Section 1.821(f) is reserved. The text previously found in this 
section is now in Sec. Sec.  1.1821(e)(1)(ii) and 1.821(e)(2)(ii).
    Section 1.821(g) is revised to delete the reference to Sec.  
1.821(f). Additionally, Sec.  1.821(g) is revised to state that any 
amendment to add or replace a ``Sequence Listing'' and CRF copy thereof 
must be submitted in accordance with the requirements of Sec.  1.825.
    Section 1.821(h) is revised to reference paragraph (e)(3) of this 
section instead of paragraphs (b) through (f). Section 1.821(h) is also 
revised to add that a late furnishing fee, as set forth in Sec.  
1.445(a)(5), is required where a ``Sequence Listing'' under PCT Rule 
13ter is provided.

Section 1.822

    Section 1.822(b) is revised to remove all prior references to WIPO 
Standard ST.25 (1998) and instead cross-reference new Appendices A 
through F to 37 CFR part 1, subpart G, which contain the updated 2009 
version of the standard. Therefore, the statement regarding permission 
for incorporation by reference and information about the availability 
of ST.25 from WIPO's website is deleted.
    Section 1.822(c)(1) is revised to remove the prior reference to 
WIPO Standard ST.25 (1998) and instead cross-reference new Appendix A 
to 37 CFR part 1, subpart G, which contains the updated 2009 version of 
the standard.
    Section 1.822(c)(3) is rewritten to replace instances of ``typed'' 
with ``listed.''
    Section 1.822(c)(5) is rewritten to replace ``presented'' with 
``represented.''
    Section 1.822(c)(6) is rewritten to delete ``be marked'' and 
instead state ``appear.''
    Section 1.822(d)(1) is revised to remove the prior reference to 
WIPO Standard ST.25 (1998) and instead cross-reference new Appendix C 
to 37 CFR part 1, subpart G, which contains the updated 2009 version of 
the standard.
    Section 1.822(d)(3) is rewritten to replace ``presented'' with 
``represented.''
    Section 1.822(d)(4) is rewritten to replace ``presented'' with 
``represented.''
    Section 1.822(d)(5) is rewritten to replace the second occurrence 
of ``presented'' with ``represented.''
    Section 1.822(e) is rewritten to replace ``that is made up'' with 
the term ``composed.''

Section 1.823

    The title of Sec.  1.823 is rewritten as ``Requirements for content 
of a `Sequence Listing' part of the specification.''
    Section 1.823(a) is rewritten to enumerate in Sec.  1.823(a)(1) 
through (8) the content requirements for a ``Sequence Listing'' 
previously contained in Sec. Sec.  1.821(c), 1.823(a)(1), 1.823(a)(2), 
and 1.823(b). Such requirements include, but are not limited to, 
sequence identifiers, the order and presentation of items of 
information, mandatory and optional information, the format as to line 
spacing, and the use of numeric identifiers.
    Section 1.823(b)(1) is revised to include a requirement for 
applications, other than an international application

[[Page 57043]]

in the international stage, to contain, in the specification of the 
patent application, an express incorporation by reference of the 
material submitted as an ASCII plain text file via the USPTO patent 
electronic filing system or on a read-only optical disc(s) identifying 
the name of the file, the date of creation, and the size of the file in 
bytes.
    Section 1.823(b)(2) is revised to specifically exempt international 
applications during the international stage from the incorporation by 
reference requirement in Sec.  1.823(b)(1).
    Section 1.823(b)(3) is added to specifically set forth the format 
and content for a ``Sequence Listing'' that is submitted either as a 
PDF image file via the USPTO patent electronic filing system or on 
physical sheets of paper, as enumerated in Sec.  1.823(b)(3)(i) through 
(vi).

Section 1.824

    The title of Sec.  1.824 is rewritten as ``Form and format for a 
nucleotide and/or amino acid sequence submission as an ASCII plain text 
file.''
    Section 1.824(a) is reorganized for clarity and to apply to any 
``Sequence Listing'' submission as an ASCII plain text file, rather 
than only to the CRF of a ``Sequence Listing.'' Section 1.824(a)(1) 
sets forth the computer compatibilities and operating systems 
permitted. Section 1.824(a)(2) indicates that ASCII plain text is 
required, that all printable characters are permitted, and that no 
nonprintable characters are permitted, except ASCII Carriage Return 
plus ASCII Line Feed (CRLF) or Line Feed (LF) as line terminators. 
Section 1.824(a)(3) sets forth the naming convention for the ASCII 
plain text file of the ``Sequence Listing.'' Section 1.824(a)(4) is 
revised to indicate that no more than 74 printable characters can be 
present on any given line. This number represents a change from current 
rules (where 72 characters are permitted). This change is intended to 
conform to the number of characters of a sequence listing as printed in 
a granted patent or a pre-grant publication.
    Section 1.824(a)(5) indicates that pagination is not permitted and 
that the ASCII plain text file must be one continuous file, with no 
hard page breaks and no page numbering.
    Section 1.824(b) indicates that the ASCII plain text file must 
contain a copy of a single ``Sequence Listing'' in a single file and 
may be submitted through either the USPTO patent electronic filing 
system or on a read-only optical disc(s), in compliance with Sec.  
1.52(e). Section 1.824(b)(2) provides that file compression may be 
used, and it defines the parameters for file compression for submission 
on a read-only optical disc. Section 1.824 is further revised to 
eliminate obsolete media on which the CRF of a ``Sequence Listing'' may 
be submitted. Section 1.824(c) is eliminated, since the types of media 
available are specifically enumerated in Sec.  1.52(e). Section 
1.824(d) is eliminated, since the same provision is now included in 
Sec.  1.52(e)(6).

Section 1.825

    Sections 1.825(a) and (b) are rewritten to distinguish between a 
newly added ``Sequence Listing'' and an amended/replacement ``Sequence 
Listing'' submission, respectively. Sections 1.825(a) and (b) are 
rewritten to state when a new or amended/replacement copy of the CRF is 
also required upon submission of a ``Sequence Listing.''
    Section 1.825(a) is amended to provide for submission of a 
``Sequence Listing'' not present on the application filing date (1) as 
an ASCII plain text file via either the USPTO patent electronic filing 
system or on a read-only optical disc, (2) as a PDF image file via the 
USPTO patent electronic filing system, or (3) on physical sheets of 
paper. The amendment adding the ``Sequence Listing'' must include a 
request that the amendment be made in one of two ways. First, a 
``Sequence Listing'' submitted as an ASCII plain text file, in 
accordance with Sec.  1.825(a)(2)(i), must be incorporated by reference 
in a separate paragraph of the specification. Second, a ``Sequence 
Listing'' submitted as a PDF image file via the USPTO patent electronic 
filing system, in accordance with Sec.  1.825(a)(2)(ii), or on physical 
sheets of paper, in accordance with Sec.  1.825(a)(2)(iii), must be 
placed after the abstract of the disclosure. Additionally, the 
``Sequence Listing'' must be submitted together with two statements. 
The first statement must indicate the basis for the amendment, with 
specific references to particular parts of the application as 
originally filed (specification, claims, drawings) for all sequence 
data in the ``Sequence Listing'' (Sec.  1.821(a)(3)). The second 
statement must indicate that the ``Sequence Listing'' contains no new 
matter (Sec.  1.821(a)(4)). Finally, if needed, Sec.  1.825(a)(5) 
provides that a new or substitute CRF must be submitted together with a 
statement, pursuant to Sec.  1.825(a)(6), that the sequence information 
contained in the CRF is the same as the sequence information contained 
in the ``Sequence Listing'' that had been submitted as a PDF image file 
via the USPTO patent electronic filing system or on physical sheets of 
paper.
    Section 1.825(b) is updated to require an amended/replacement 
``Sequence Listing'' be submitted (1) as an ASCII plain text file via 
either the USPTO patent electronic filing system or on a read-only 
optical disc (Sec.  1.825(b)(1)(i)), (2) as a PDF image file via the 
USPTO patent electronic filing system (Sec.  1.825(b)(1)(ii)), or (3) 
on physical sheets of paper (Sec.  1.825(b)(1)(iii)). The amended/
replacement ``Sequence Listing'' must include a request that it be made 
in one of two ways. First, the request can ask to incorporate by 
reference the amended/replacement ``Sequence Listing,'' submitted as an 
ASCII plain text file, in a separate paragraph of the specification 
(replacing any prior such paragraph, as applicable) (Sec.  
1.825(b)(2)). Second, the request can ask to insert, after the abstract 
of the disclosure, the amended/replacement ``Sequence Listing'' that 
was submitted as a PDF image file via the USPTO patent electronic 
filing system or on physical sheets of paper (replacing any prior 
``Sequence Listing,'' as applicable).
    The amended/replacement ``Sequence Listing'' must be submitted 
together with three statements. The first statement must identify the 
location of all deletions, replacements, or additions to the ``Sequence 
Listing'' (Sec.  1.825(b)(3)). The second statement must indicate the 
basis for the amendment, with specific references to particular parts 
of the application as originally filed (specification, claims, 
drawings) for all amended sequence data in the replacement ``Sequence 
Listing'' (Sec.  1.825(b)(4)). The third statement must indicate that 
the replacement ``Sequence Listing'' contains no new matter (Sec.  
1.825(b)(5)). Finally, if needed, a new or substitute CRF with the 
amendment incorporated therein (Sec.  1.825(b)(6)) must be submitted 
together with a statement that the sequence information contained in 
the CRF is the same as the sequence information contained in the 
replacement ``Sequence Listing'' submitted as a PDF image file via the 
USPTO patent electronic filing system or on physical sheets of paper 
(Sec.  1.825(b)(7)).
    Section 1.825(c) replaces the current Sec.  1.825(c), which is 
moved to Sec.  1.825(d). Section 1.825(c) relates to the required 
incorporation by reference statement when submitting a ``Sequence 
Listing'' under Sec.  1.821(c)(1). Should the application as originally 
filed not contain the incorporation by reference, it must be amended to 
contain such an incorporation by reference.
    Section 1.825(d) contains the material from the current Sec.  
1.825(c).

[[Page 57044]]

Subpart G of Part 1

    Appendices A through F are added, explicitly incorporating the text 
of Tables 1-6, Appendix 2, WIPO Standard ST.25 (2009) into the CFR. 
Appendix G is added to incorporate the table that was previously 
located in Sec.  1.823.

Comments and Responses

    The USPTO published a proposed rule on May 26, 2021, at 86 FR 
28301, soliciting public comment on the proposed amendments to 37 CFR 
part 1 being adopted in this final rule. The USPTO received no comments 
from the public on the proposed rule.

Rulemaking Considerations

A. Administrative Procedure Act

    The changes in this rulemaking involve rules of agency practice and 
procedure, and/or interpretive rules. See Bachow Commc'ns Inc. v. FCC, 
237 F.3d 683, 690 (D.C. Cir. 2001) (rules governing an application 
process are procedural under the Administrative Procedure Act); Inova 
Alexandria Hosp. v. Shalala, 244 F.3d 342, 350 (4th Cir. 2001) (rules 
for handling appeals are procedural where they do not change the 
substantive standard for reviewing claims); Nat'l Org. of Veterans' 
Advocates v. Sec'y of Veterans Affairs, 260 F.3d 1365, 1375 (Fed. Cir. 
2001) (rule that clarifies interpretation of a statute is 
interpretive).
    Accordingly, prior notice and opportunity for public comment for 
the changes in this rulemaking were not required pursuant to 5 U.S.C. 
553(b) or (c), or any other law. See Cooper Techs. Co. v. Dudas, 536 
F.3d 1330, 1336-37 (Fed. Cir. 2008) (stating that 5 U.S.C. 553, and 
thus 35 U.S.C. 2(b)(2)(B), do not require notice and comment rulemaking 
for ``interpretative rules, general statements of policy, or rules of 
agency organization, procedure, or practice'' (quoting 5 U.S.C. 
553(b)(A))). However, the USPTO chose to seek public comment before 
implementing the rule to benefit from the public's input.

B. Regulatory Flexibility Act

    For the reasons set forth herein, the Senior Counsel for Regulatory 
and Legislative Affairs of the USPTO has certified to the Chief Counsel 
for Advocacy of the Small Business Administration that this rule will 
not have a significant economic impact on a substantial number of small 
entities. See 5 U.S.C. 605(b).
    The USPTO amends the rules of practice to permit higher-capacity 
physical media to be submitted to accommodate patent applications for 
certain inventions that require significant data in ASCII plain text 
format that exceed the capacity of the Office's electronic filing 
system. Additionally, extraction of compressed data files, which had 
not been permitted in the past for certain submissions, is permitted if 
compliant with certain new procedures. Other rules related to certain 
obsolete and non-secure methods of presenting data are eliminated. 
Lastly, this rule removes an applicant's ability to rely on a 
previously submitted CRF of required sequence information (i.e., CRF 
transfer requests are eliminated). In light of the ability to download 
a ``Sequence Listing'' from granted U.S. patents and U.S. patent 
application publications via Public PAIR in the Supplemental Content 
tab, there is no longer a need for a CRF transfer.
    This rulemaking makes more flexible the process for submitting 
large amounts of data and streamlines other procedural steps related to 
data files associated with patent applications. This rulemaking's 
changes are largely procedural in nature and do not impose any 
additional requirements or fees on applicants. For the foregoing 
reasons, the changes in this rule will not have a significant economic 
impact on a substantial number of small entities.

C. Executive Order 12866 (Regulatory Planning and Review)

    This rulemaking has been determined to be not significant for 
purposes of Executive Order 12866 (Sept. 30, 1993).

D. Executive Order 13563 (Improving Regulation and Regulatory Review)

    The USPTO has complied with Executive Order 13563 (Jan. 18, 2011). 
Specifically, to the extent feasible and applicable, the USPTO has: (1) 
Reasonably determined that the benefits of the rule justify its costs; 
(2) tailored the rule to impose the least burden on society consistent 
with obtaining the agency's regulatory objectives; (3) selected a 
regulatory approach that maximizes net benefits; (4) specified 
performance objectives; (5) identified and assessed available 
alternatives; (6) involved the public in an open exchange of 
information and perspectives among experts in relevant disciplines, 
affected stakeholders in the private sector, and the public as a whole, 
and provided online access to the rulemaking docket; (7) attempted to 
promote coordination, simplification, and harmonization across 
Government agencies and identified goals designed to promote 
innovation; (8) considered approaches that reduce burdens while 
maintaining flexibility and freedom of choice for the public; and (9) 
ensured the objectivity of scientific and technological information and 
processes.

E. Executive Order 13132 (Federalism)

    This rulemaking does not contain policies with federalism 
implications sufficient to warrant preparation of a Federalism 
Assessment under Executive Order 13132 (Aug. 4, 1999).

F. Executive Order 13175 (Tribal Consultation)

    This rulemaking will not (1) have substantial direct effects on one 
or more Indian tribes, (2) impose substantial direct compliance costs 
on Indian tribal governments, or (3) preempt tribal law. Therefore, a 
tribal summary impact statement is not required under Executive Order 
13175 (Nov. 6, 2000).

G. Executive Order 13211 (Energy Effects)

    This rulemaking is not a significant energy action under Executive 
Order 13211 because this rulemaking is not likely to have a significant 
adverse effect on the supply, distribution, or use of energy. 
Therefore, a Statement of Energy Effects is not required under 
Executive Order 13211 (May 18, 2001).

H. Executive Order 12988 (Civil Justice Reform)

    This rulemaking meets applicable standards to minimize litigation, 
eliminate ambiguity, and reduce burden as set forth in sections 3(a) 
and 3(b)(2) of Executive Order 12988 (Feb. 5, 1996).

I. Executive Order 13045 (Protection of Children)

    This rulemaking does not concern an environmental risk to health or 
safety that may disproportionately affect children under Executive 
Order 13045 (Apr. 21, 1997).

J. Executive Order 12630 (Taking of Private Property)

    This rulemaking will not effect a taking of private property or 
otherwise have taking implications under Executive Order 12630 (Mar. 
15, 1988).

K. Congressional Review Act

    Under the Congressional Review Act provisions of the Small Business 
Regulatory Enforcement Fairness Act of 1996 (5 U.S.C. 801 et seq.), the 
USPTO will submit a report containing the final rule and other required 
information to the United States Senate, the United States House of 
Representatives, and the Comptroller General of the Government 
Accountability Office. The changes in this rulemaking are not expected 
to

[[Page 57045]]

result in an annual effect on the economy of $100 million or more, a 
major increase in costs or prices, or significant adverse effects on 
competition, employment, investment, productivity, innovation, or the 
ability of United States-based enterprises to compete with foreign-
based enterprises in domestic and export markets. Therefore, this 
rulemaking is not expected to result in a ``major rule'' as defined in 
5 U.S.C. 804(2).

L. Unfunded Mandates Reform Act of 1995

    The changes set forth in this rulemaking do not involve a Federal 
intergovernmental mandate that will result in the expenditure by State, 
local, and tribal governments, in the aggregate, of $100 million (as 
adjusted) or more in any one year, or a Federal private sector mandate 
that will result in the expenditure by the private sector of $100 
million (as adjusted) or more in any one year, and will not 
significantly or uniquely affect small governments. Therefore, no 
actions are necessary under the provisions of the Unfunded Mandates 
Reform Act of 1995. See 2 U.S.C. 1501 et seq.

M. National Environmental Policy Act of 1969

    This rulemaking will not have any effect on the quality of the 
environment and is thus categorically excluded from review under the 
National Environmental Policy Act of 1969. See 42 U.S.C. 4321 et seq.

N. National Technology Transfer and Advancement Act of 1995

    The requirements of section 12(d) of the National Technology 
Transfer and Advancement Act of 1995 (15 U.S.C. 272 note) are not 
applicable because this rulemaking does not contain provisions that 
involve the use of technical standards.

O. Paperwork Reduction Act of 1995

    The Paperwork Reduction Act of 1995 (44 U.S.C. 3501-3549) requires 
that the USPTO consider the impact of paperwork and other information 
collection burdens imposed on the public. In accordance with section 
3507(d) of the Paperwork Reduction Act of 1995, the majority of the 
paperwork and other information collection burdens discussed in this 
rule have already been approved under the following Office of 
Management and Budget (OMB) Control Numbers: 0651-0024 (Sequence 
Listing), 0651-0031 (Patent Processing), 0651-0032 (Initial Patent 
Applications), and 0651-0064 (Patent Reexaminations and Supplemental 
Examinations).
    Modifications to 0651-0024 because of this rulemaking have been 
submitted to OMB. Modifications include the removal of the Request for 
Transfer of a Computer Readable Form Under 37 CFR 1.821(e) (Form PTO/
SB/93), which will result in a slight reduction in the burden 
associated with this information collection. The USPTO estimates that 
this information collection's annual burden will decrease by 1,550 
responses and 155 burden hours. These burden reduction estimates are 
based on the prior OMB approved burdens (response volumes) associated 
with this information collection, which may be different from any 
forecasts mentioned in other parts of this rule.
    The changes discussed in this rule do not affect the information 
collection requirements or burdens associated with 0651-0031, 0651-
0032, and 0651-0064 listed above; therefore, the USPTO has not taken 
any additional actions on these information collections as a result of 
this rulemaking. Notwithstanding any other provision of law, no person 
is required to respond to, nor shall a person be subject to a penalty 
for failure to comply with, a collection of information subject to the 
requirements of the Paperwork Reduction Act unless that collection of 
information has a currently valid OMB control number.

P. E-Government Act Compliance

    The USPTO is committed to compliance with the E-Government Act to 
promote the use of the internet and other information technologies, to 
provide increased opportunities for citizen access to Government 
information and services, and for other purposes.

List of Subjects in 37 CFR Part 1

    Administrative practice and procedure, Biologics, Courts, Freedom 
of information, Inventions and patents, Reporting and recordkeeping 
requirements, Small businesses.

    For the reasons stated in the preamble and under the authority 
contained in 35 U.S.C. 2, as amended, the USPTO amends 37 CFR part 1 as 
follows:

PART 1--RULES OF PRACTICE IN PATENT CASES

0
1. The authority citation for part 1 continues to read as follows:

    Authority: 35 U.S.C. 2(b)(2), unless otherwise noted.


0
2. Amend Sec.  1.52 by revising the section heading and paragraphs (e) 
and (f) to read as follows:


Sec.  1.52   Language, paper, writing, margins, read-only optical disc 
specifications.

* * * * *
    (e) Electronic documents submitted on a read-only optical disc that 
are to become part of the permanent United States Patent and Trademark 
Office records in the file of a patent application, reexamination, or 
supplemental examination proceeding. (1) The following documents may be 
submitted to the Office on a read-only optical disc in compliance with 
this paragraph (e):
    (i) A ``Computer Program Listing Appendix'' (see Sec.  1.96(c));
    (ii) A ``Sequence Listing'' (submitted under Sec.  1.821(c) in 
compliance with Sec.  1.824); or
    (iii) ``Large Tables'' (see Sec.  1.58(c)).
    (2) Read-only optical disc as used in this part means a finalized 
disc, in conformance with International Organization for 
Standardization (ISO) 9660, on which the data is recorded so it is 
permanent and cannot be changed or erased, and is one of:
    (i) Compact Disc-Read-Only Memory (CD-ROM) or a Compact Disc-
Recordable (CD-R); or
    (ii) Digital Video Disc-Recordable (DVD-R or DVD+R);
    (3) Each read-only optical disc must conform to the following 
requirements:
    (i) Computer compatibility: PC or Mac[supreg];
    (ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], MacOS[supreg], or Unix[supreg]/Linux[supreg]; and
    (iii) The contents of each read-only optical disc must be in 
American Standard Code for Information Interchange (ASCII) plain text 
and if compressed, must be compressed in accordance with Sec. Sec.  
1.58, 1.96, and 1.824, as applicable.
    (4) Each read-only optical disc must be enclosed in a hard case 
within an unsealed, padded, and protective mailing envelope, and must 
be accompanied by a transmittal letter in accordance with paragraph (a) 
of this section, including the following information:
    (i) First-named inventor (if known);
    (ii) Title of the invention;
    (iii) Attorney docket or file reference number (if applicable);
    (iv) Application number and filing date (if known);
    (v) The operating system (MS-DOS[supreg], MS-Windows[supreg], Mac 
OS[supreg], or Unix[supreg]/Linux[supreg]) used to produce the disc; 
and
    (vi) The file(s) contained on the read-only optical disc, including 
the name of the file, the size of the file in bytes, and the date of 
creation.
    (5) Each read-only optical disc must have a label permanently 
affixed thereto

[[Page 57046]]

on which the following information has been hand-printed or typed:
    (i) First-named inventor (if known);
    (ii) Title of the invention;
    (iii) Attorney docket or file reference number (if applicable);
    (iv) Application number and filing date (if known);
    (v) Date on which the data were recorded on the read-only optical 
disc; and
    (vi) Disc order (e.g., ``1 of X''), if multiple read-only optical 
discs are submitted.
    (6) Read-only optical discs will not be returned to the applicant 
and may not be retained as part of the patent application file.
    (7) Any amendment to the information on a read-only optical disc 
must be by way of a replacement read-only optical disc, in compliance 
with Sec.  1.58(g) for ``Large Tables,'' Sec.  1.96(c)(5) for a 
``Computer Program Listing Appendix,'' and Sec.  1.825(b) for a 
``Sequence Listing'' or Computer Readable Form (CRF) of a ``Sequence 
Listing.''
    (8) The specification must contain an incorporation by reference of 
the material on each read-only optical disc in a separate paragraph 
(Sec.  1.77(b)(5)), identifying the name of each file, their date of 
creation, and their size in bytes, except for an international 
application in the international stage. The Office may require the 
applicant to amend the specification to include the material 
incorporated by reference.
    (9) If a file is unreadable, it will be treated as not having been 
submitted, and a notice will be issued to require a compliant 
submission.
    (f) Determining application size fees for applications containing 
electronic documents submitted on a read-only optical disc or via the 
USPTO patent electronic filing system--(1) Submission on Read-Only 
Optical Discs: The application size fee required by Sec.  1.16(s) or 
1.492(j), for an application component submitted in part on a read-only 
optical disc in compliance with paragraph (e) of this section, shall be 
determined such that each three kilobytes of content submitted on a 
read-only optical disc shall be counted as a sheet of paper. Excluded 
from this determination is any ASCII plain text file submitted on a 
read-only optical disc under paragraph (e) of this section containing:
    (i) Any ``Sequence Listing'' or CRF of a ``Sequence Listing'' in 
compliance with Sec.  1.821(c) or (e); or
    (ii) Any ``Computer Program Listing Appendix'' in compliance with 
Sec.  1.96(c).
    (2) Submission via the USPTO Patent Electronic Filing System: The 
application size fee required by Sec.  1.16(s) or Sec.  1.492(j), for 
an application submitted in whole or in part via the USPTO patent 
electronic filing system, shall be determined such that the paper size 
equivalent will be considered to be 75% of the number of sheets of 
paper present in the specification and drawings in the application when 
entered into the Office file wrapper after being rendered by the USPTO 
patent electronic filing system. Excluded from this determination is 
any ASCII plain text file submitted via the USPTO patent electronic 
filing system containing:
    (i) Any ``Sequence Listing'' or CRF of a ``Sequence Listing'' in 
compliance with Sec.  1.821(c) or (e); or
    (ii) Any ``Computer Program Listing Appendix'' in compliance with 
Sec.  1.96(c).
    (3) Oversized submission. Any submission of a ``Sequence Listing'' 
in electronic form of 300 MB-800 MB filed in an application under 35 
U.S.C. 111 or 371 will be subject to the fee set forth in Sec.  
1.21(o)(1). Any submission of a ``Sequence Listing'' filed in 
electronic form that exceeds 800 MB in an application under 35 U.S.C. 
111 or 371 will be subject to the fee set forth in Sec.  1.21(o)(2).

0
3. Amend Sec.  1.58 by revising paragraphs (b) and (c) and adding 
paragraphs (d) through (j) to read as follows:


Sec.  1.58   Chemical and mathematical formulas and tables.

* * * * *
    (b) Chemical and mathematical formulas and tables must be presented 
in compliance with Sec.  1.52(a) and (b), except that chemical and 
mathematical formulas or tables may be placed in a landscape 
orientation if they cannot be presented satisfactorily in a portrait 
orientation. Typewritten characters used in such formulas and tables 
must be chosen from a block (nonscript) type font or lettering style 
having capital letters that should be at least 0.422 cm (0.166 inches) 
high (e.g., preferably Arial, Times Roman, or Courier, with a font size 
of 12 points), but may be no smaller than 0.21cm (0.08 inches) high 
(e.g., a font size of 6 points). A space at least 0.64 cm (0.25 inches) 
high should be provided between complex formulas and tables and the 
text. Chemical and mathematical formulas must be configured to maintain 
the proper positioning of their characters when displayed in order to 
preserve their intended meaning. Tables should have the lines and 
columns of data closely spaced to conserve space, consistent with a 
high degree of legibility.
    (c) The following ``Large Tables'' may be submitted in electronic 
form in ASCII plain text via the USPTO patent electronic filing system 
or on a read-only optical disc, in compliance with Sec.  1.52(e), 
excluding an international application during the international stage:
    (1) Any individual table that is more than 50 pages in length; or
    (2) Multiple tables, if the total number of pages of all the tables 
in an application exceeds 100 pages in length, where a table page is a 
page printed on paper, in conformance with paragraph (b) of this 
section.
    (d) ``Large Tables'' submitted in electronic form in ASCII plain 
text must conform to the following requirements:
    (1) Must maintain the spatial relationships (e.g., alignment of 
columns and rows) of the table elements when displayed to visually 
preserve the relational information they convey;
    (2) Must have the following compatibilities:
    (i) Computer compatibility: PC or Mac[supreg];
    (ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg].
    (3) Must be in ASCII plain text, where:
    (i) All printable characters (including the space character) are 
permitted;
    (ii) No nonprintable (ASCII control) characters are permitted, 
except ASCII Carriage Return plus ASCII Line Feed (CRLF) or Line Feed 
(LF) as line terminators.
    (4) Must be named as *.txt, where ``*'' is one character or a 
combination of characters limited to upper- or lowercase letters, 
numbers, hyphens, and underscores and does not exceed 60 characters in 
total, excluding the extension. No spaces or other types of characters 
are permitted in the file name; and
    (5) Must be incorporated by reference in a separate paragraph of 
the specification, in accordance with Sec.  1.77(b)(5).
    (e) ``Large Tables'' submitted via the USPTO patent electronic 
filing system must not exceed 25 MB, and file compression is not 
permitted.
    (f) ``Large Tables'' submitted in compliance with Sec.  1.52(e) via 
read-only optical disc must meet the following requirements:
    (1) The ASCII plain text file may be compressed using 
WinZip[supreg], 7-Zip, or Unix[supreg]/Linux[supreg] Zip;
    (2) A compressed file must not be self-extracting; and
    (3) A compressed ASCII plain text file that does not fit on a 
single read-only

[[Page 57047]]

optical disc may be split into multiple file parts in accordance with 
the target read-only optical disc size and labeled in compliance with 
Sec.  1.52(e)(5)(vi).
    (g) Any amendments to ``Large Tables'' in electronic form in ASCII 
plain text format must include:
    (1) A replacement ASCII plain text file, in accordance with the 
requirements of paragraphs (d) through (f) of this section, submitted 
via the USPTO patent electronic filing system or on a read-only optical 
disc, in compliance with Sec.  1.52(e), labeled as ``REPLACEMENT MM/DD/
YYYY'' (with the month, day, and year of creation indicated);
    (2) A request that the amendment be made by incorporation by 
reference of the material in the replacement ASCII plain text file, in 
a separate paragraph of the specification (replacing any prior such 
paragraph, as applicable) identifying the name of the file, the date of 
creation, and the size of the file in bytes (see Sec.  1.77(b)(5));
    (3) A statement that identifies the location of all deletions, 
replacements, or additions to the ASCII plain text file; and
    (4) A statement that the replacement ASCII plain text file contains 
no new matter.
    (h) The specification of an application with ``Large Tables'' as an 
ASCII plain text file, present on the application filing date, without 
an incorporation by reference of the material contained in the ASCII 
plain text file, must be amended to contain a separate paragraph 
incorporating by reference the material contained in the ASCII plain 
text file, in accordance with Sec.  1.77(b)(5).
    (i) Any read-only optical disc for ``Large Tables'' must be 
submitted in duplicate. The read-only optical disc and duplicate copy 
must be labeled ``Copy 1'' and ``Copy 2,'' respectively. The 
transmittal letter that accompanies the read-only optical discs must 
include a statement that the two read-only optical discs are identical. 
In the event that the two read-only optical disc copies are not 
identical, the Office will use the read-only optical disc labeled 
``Copy 1'' for further processing.
    (j) Any amendment to the information on a read-only optical disc 
must be by way of a replacement read-only optical disc, in compliance 
with paragraph (g) of this section, where the replacement read-only 
optical disc and copy must be labeled ``COPY 1 REPLACEMENT MM/DD/YYYY'' 
(with the month, day, and year of creation indicated), and ``COPY 2 
REPLACEMENT MM/DD/YYYY,'' respectively.

0
4. Amend Sec.  1.71 by revising paragraph (f) to read as follows:


Sec.  1.71   Detailed description and specification of the invention.

* * * * *
    (f) The specification must commence on a separate sheet. Each sheet 
including part of the specification may not include other parts of the 
application or other information. The claim(s), abstract, and 
``Sequence Listing'' (if required or submitted under Sec.  1.821(c)) 
should not be included on a sheet including any other part of the 
application.
* * * * *

0
5. Amend Sec.  1.77 by revising paragraphs (b)(5) and (13) to read as 
follows:


Sec.  1.77   Arrangement of application elements.

* * * * *
    (b) * * *
    (5) An incorporation by reference statement regarding the material 
in the one or more ASCII plain text files, submitted via the USPTO 
patent electronic filing system or on one or more read-only optical 
discs (see Sec.  1.52(e)(8)), identifying the names of each file, the 
date of creation of each file, and the size of each file in bytes, for 
the following document types:
    (i) A ``Computer Program Listing Appendix'' (see Sec.  1.96(c));
    (ii) A ``Sequence Listing'' (see Sec.  1.821(c)); or
    (iii) ``Large Tables'' (see Sec.  1.58(c)).
* * * * *
    (13) ``Sequence Listing,'' required by Sec.  1.821(c), that is 
submitted as a Portable Document Format (PDF) file (as set forth in 
Sec.  1.821(c)(1)(ii)) via the USPTO patent electronic filing system or 
on physical sheets of paper (as set forth in Sec.  1.821(c)(1)(iii)).
* * * * *

0
6. Amend Sec.  1.96 by revising paragraphs (a) and (c) to read as 
follows:


Sec.  1.96   Submission of computer program listings.

    (a) General. Descriptions of the operation and general content of 
computer program listings should appear in the description portion of 
the specification. A computer program listing for the purpose of this 
section is defined as a document that lists, in appropriate sequence, 
the instructions, routines, and other contents of a program for a 
computer. The program listing may be either in machine or machine-
independent (object or source) language that will cause a computer to 
perform a desired procedure or task such as solving a problem, 
regulating the flow of work in a computer, or controlling or monitoring 
events. Computer program listings may be submitted in patent 
applications, as set forth in paragraphs (b) and (c) of this section.
* * * * *
    (c) As an appendix that will not be printed: Any computer program 
listing may, and any computer program listing having over 300 lines (up 
to 72 characters per line) must, be submitted as an electronic document 
in ASCII plain text, whether submitted via the USPTO patent electronic 
filing system or on a read-only optical disc, in compliance with Sec.  
1.52(e). An electronic document containing such a computer program 
listing is to be referred to as a ``Computer Program Listing 
Appendix.'' The ``Computer Program Listing Appendix'' will not be part 
of the printed patent. The specification must include an incorporation 
by reference of the ``Computer Program Listing Appendix,'' in 
accordance with Sec.  1.77(b)(5).
    (1) A ``Computer Program Listing Appendix'' must conform to the 
following requirements:
    (i) Computer compatibility: PC or Mac[supreg];
    (ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg];
    (iii) Line terminator: ASCII CRLF or LF only; and
    (iv) Control codes: The data must not be dependent on control 
characters or codes that are not defined in the ASCII character set.
    (2) Each file must be named as *.txt, where ``*'' is one character 
or a combination of characters limited to upper- or lowercase letters, 
numbers, hyphens, and underscores and does not exceed 60 characters in 
total, excluding the extension. No spaces or other types of characters 
are permitted in the file name.
    (3) Each file containing a ``Computer Program Listing Appendix'' 
submitted via the USPTO patent electronic filing system must not exceed 
25 MB, and file compression is not permitted.
    (4) A ``Computer Program Listing Appendix'' submitted in compliance 
with Sec.  1.52(e) must conform to the following requirements:
    (i) A separate read-only optical disc containing a ``Computer 
Program Listing Appendix'' must be submitted for each applicable 
application;
    (ii) Multiple computer program listings for a single application 
may be placed on a single read-only optical disc;
    (iii) Multiple read-only optical discs, containing one or more 
computer

[[Page 57048]]

program listings, may be submitted for a single application, if 
necessary;
    (iv) Any computer program listing may, and a computer program 
listing having a nested file structure must, when submitted in 
compliance with Sec.  1.52(e), be compressed into a single file using 
WinZip[supreg], 7-Zip, or Unix[supreg]/Linux[supreg] Zip;
    (v) Any compressed file must not be self-extracting; and
    (vi) A compressed ASCII plain text file that does not fit on a 
single read-only optical disc may be split into multiple file parts, in 
accordance with the target read-only optical disc size and labeled in 
compliance with Sec.  1.52(e)(5)(vi).
    (5) Any amendments to a ``Computer Program Listing Appendix'' in 
electronic form in ASCII plain text format must include:
    (i) A replacement ASCII plain text file, in accordance with the 
requirements of this paragraph (c), submitted via the USPTO patent 
electronic filing system, or on a read-only optical disc, in compliance 
with Sec.  1.52(e), where the replacement read-only optical disc must 
be submitted in duplicate, and the read-only optical discs must be 
labeled ``COPY 1 REPLACEMENT MM/DD/YYYY'' (with the month, day, and 
year of creation indicated) and ``COPY 2 REPLACEMENT MM/DD/YYYY'';
    (ii) A request that the amendment be made by incorporation by 
reference of the material in the replacement ASCII plain text file, in 
a separate paragraph of the specification (replacing any prior such 
paragraph) identifying the name of the file, the date of creation, and 
the size of the file in bytes (see Sec.  1.77(b)(5));
    (iii) A statement that identifies the location of all deletions, 
replacements, or additions to the ASCII plain text file; and
    (iv) A statement that the replacement ASCII plain text file 
contains no new matter.
    (6) The specification of a complete application with a ``Computer 
Program Listing Appendix'' as an ASCII plain text file, filed on the 
application filing date, without an incorporation by reference of the 
material contained in the ASCII plain text file, must be amended to 
contain a separate paragraph incorporating by reference the material 
contained in the ASCII plain text file, in accordance with Sec.  
1.77(b)(5).
    (7) Any read-only optical disc for a ``Computer Program Listing 
Appendix'' must be submitted in duplicate. The read-only optical disc 
and duplicate copy must be labeled ``Copy 1'' and ``Copy 2,'' 
respectively. The transmittal letter that accompanies the read-only 
optical discs must include a statement that the two read-only optical 
discs are identical. In the event that the two read-only optical discs 
are not identical, the Office will use the read-only optical disc 
labeled ``Copy 1'' for further processing. Any amendment to the 
information on a read-only optical disc must be by way of a replacement 
read-only optical disc, in compliance with Sec.  1.96(c)(5).

0
7. Amend Sec.  1.121 by revising paragraph (b) introductory text and 
adding paragraph (b)(6) to read as follows:


Sec.  1.121   Manner of making amendments in applications.

* * * * *
    (b) Specification. Amendments to the specification, other than the 
claims, ``Large Tables'' (Sec.  1.58(c)), a ``Computer Program Listing 
Appendix'' (Sec.  1.96(c)(5) and (7)), and a ``Sequence Listing'' or 
CRF (Sec.  1.825), must be made by adding, deleting, or replacing a 
paragraph; by replacing a section; or by a substitute specification 
(Sec.  1.125), in the manner specified in this section.
* * * * *
    (6) Changes to ``Large Tables,'' a ``Computer Program Listing 
Appendix,'' or a ``Sequence Listing'' must be made in accordance with 
Sec.  1.58(g) for ``Large Tables,'' Sec.  1.96(c)(5) for a ``Computer 
Program Listing Appendix,'' and Sec.  1.825 for a ``Sequence Listing.''
* * * * *

0
8. Amend Sec.  1.173 by revising paragraphs (b)(1) and (d) to read as 
follows:


Sec.  1.173   Reissue specification, drawings, and amendments.

* * * * *
    (b) * * *
    (1) Specification other than the claims, ``Large Tables'' (Sec.  
1.58(c)), a ``Computer Program Listing Appendix'' (Sec.  1.96(c)), or a 
``Sequence Listing'' (Sec.  1.821(c)). (i) Changes to the 
specification, other than to the claims, ``Large Tables'' (Sec.  
1.58(c)), a ``Computer Program Listing Appendix'' (Sec.  1.96(c)), or a 
``Sequence Listing'' (Sec.  1.821(c)), must be made by submission of 
the entire text of an added or rewritten paragraph, including markings 
pursuant to paragraph (d) of this section, except that an entire 
paragraph may be deleted by a statement deleting the paragraph, without 
presentation of the text of the paragraph. The precise point in the 
specification where any added or rewritten paragraph is located must be 
identified.
    (ii) Changes to ``Large Tables,'' a ``Computer Program Listing 
Appendix,'' or a ``Sequence Listing'' must be made in accordance with 
Sec.  1.58(g) for ``Large Tables,'' Sec.  1.96(c)(5) for a ``Computer 
Program Listing Appendix,'' and Sec.  1.825 for a ``Sequence Listing.''
* * * * *
    (d) Changes shown by markings. Any changes relative to the patent 
being reissued that are made to the specification, including the claims 
but excluding ``Large Tables,'' a ``Computer Program Listing 
Appendix,'' or a ``Sequence Listing,'' upon filing or by an amendment 
paper in the reissue application, must include the following markings:
    (1) The matter to be omitted by reissue must be enclosed in 
brackets; and
    (2) The matter to be added by reissue must be underlined.
* * * * *

0
9. Amend Sec.  1.530 by revising paragraph (d)(1) to read as follows:


Sec.  1.530   Statement by patent owner in ex parte reexamination; 
amendment by patent owner in ex parte or inter partes reexamination; 
inventorship change in ex parte or inter partes reexamination.

* * * * *
    (d) * * *
    (1) Specification other than the claims, ``Large Tables'' (Sec.  
1.58(c)), a ``Computer Program Listing Appendix'' (Sec.  1.96(c)), or a 
``Sequence Listing'' (Sec.  1.821(c)). (i) Changes to the 
specification, other than to the claims, ``Large Tables'' (Sec.  
1.58(c)), a ``Computer Program Listing Appendix'' (Sec.  1.96(c)), or a 
``Sequence Listing'' (Sec.  1.821(c)), must be made by submission of 
the entire text of an added or rewritten paragraph, including markings 
pursuant to paragraph (f) of this section, except that an entire 
paragraph may be deleted by a statement deleting the paragraph, without 
presentation of the text of the paragraph. The precise point in the 
specification where any added or rewritten paragraph is located must be 
identified.
    (ii) Changes to ``Large Tables,'' a ``Computer Program Listing 
Appendix,'' or a ``Sequence Listing'' must be made in accordance with 
Sec.  1.58(g) for ``Large Tables,'' Sec.  1.96(c)(5) for a ``Computer 
Program Listing Appendix,'' and Sec.  1.825 for a ``Sequence Listing.''
* * * * *

0
10. Amend Sec.  1.821 by revising paragraphs (a) and (c) through (e), 
removing and reserving paragraph (f), and revising paragraphs (g) and 
(h) to read as follows:

[[Page 57049]]

Sec.  1.821   Nucleotide and/or amino acid sequence disclosures in 
patent applications.

    (a) Nucleotide and/or amino acid sequences, as used in Sec. Sec.  
1.821 through 1.825, are interpreted to mean an unbranched sequence of 
4 or more amino acids or an unbranched sequence of 10 or more 
nucleotides. Branched sequences are specifically excluded from this 
definition. Sequences with fewer than four specifically defined 
nucleotides or amino acids are specifically excluded from this section. 
``Specifically defined'' means those amino acids other than ``Xaa'' and 
those nucleotide bases other than ``n,'' defined in accordance with 
Appendices A through F to this subpart. Nucleotides and amino acids are 
further defined as follows:
    (1) Nucleotides. Nucleotides are intended to embrace only those 
nucleotides that can be represented using the symbols set forth in 
Appendix A to this subpart. Modifications (e.g., methylated bases) may 
be described as set forth in Appendix B to this subpart but shall not 
be shown explicitly in the nucleotide sequence.
    (2) Amino acids. Amino acids are those L-amino acids commonly found 
in naturally occurring proteins and are listed in appendix C to this 
subpart. Those amino acid sequences containing D-amino acids are not 
intended to be embraced by this definition. Any amino acid sequence 
that contains post-translationally modified amino acids may be 
described as the amino acid sequence that is initially translated using 
the symbols shown in appendix C to this subpart, with the modified 
positions (e.g., hydroxylations or glycosylations) being described as 
set forth in appendix D to this subpart, but these modifications shall 
not be shown explicitly in the amino acid sequence. Any peptide or 
protein that can be expressed as a sequence using the symbols in 
appendix C to this subpart, in conjunction with a description in the 
Feature section, to describe, for example, modified linkages, cross 
links and end caps, non-peptidyl bonds, etc., is embraced by this 
definition.

    Note 1 to paragraph (a):  Appendices A through F to this subpart 
contain Tables 1-6 of the World Intellectual Property Organization 
(WIPO) Handbook on Industrial Property Information and 
Documentation, Standard ST.25: Standard for the Presentation of 
Nucleotide and Amino Acid Sequence Listings in Patent Applications 
(2009).

* * * * *
    (c) Patent applications that contain disclosures of nucleotide and/
or amino acid sequences, as defined in paragraph (a) of this section, 
must contain a ``Sequence Listing,'' which is a separate part of the 
specification containing each of those nucleotide and/or amino acid 
sequences and associated information using the symbols and format in 
accordance with the requirements of Sec. Sec.  1.822 and 1.823. The 
``Sequence Listing'' must be submitted as follows, except for a 
national stage entry under Sec.  1.495(b)(1), where the ``Sequence 
Listing'' has been previously communicated by the International Bureau 
or originally filed in the United States Patent and Trademark Office 
and complies with Patent Cooperation Treaty (PCT) Rule 5.2:
    (1) As an ASCII plain text file, in compliance with Sec.  1.824, 
submitted via the USPTO patent electronic filing system or on a read-
only optical disc under Sec.  1.52(e), accompanied by an incorporation 
by reference statement of the ASCII plain text file, in a separate 
paragraph of the specification, in accordance with Sec.  1.77(b)(5);
    (2) As a PDF file via the USPTO patent electronic filing system; or
    (3) On physical sheets of paper.
    (d) Where the description or claims of a patent application discuss 
a sequence that is set forth in the ``Sequence Listing,'' in accordance 
with paragraph (c) of this section, reference must be made to the 
sequence by use of a sequence identifier (Sec.  1.823(a)(5)), preceded 
by ``SEQ ID NO:'' or the like, in the text of the description or 
claims, even if the sequence is also embedded in the text of the 
description or claims of the patent application. Where a sequence is 
presented in a drawing, reference must be made to the sequence by use 
of the sequence identifier (Sec.  1.823(a)(5)), either in the drawing 
or in the Brief Description of the Drawings, where the correlation 
between multiple sequences in the drawing and their sequence 
identifiers (Sec.  1.823(a)(5)) in the Brief Description is clear.
    (e)(1) If the ``Sequence Listing'' under paragraph (c) of this 
section is submitted in an application filed under 35 U.S.C. 111(a) as 
a PDF file (Sec.  1.821(c)(2)) via the USPTO patent electronic filing 
system or on physical sheets of paper (Sec.  1.821(c)(3)), then the 
following must be submitted:
    (i) A CRF of the ``Sequence Listing,'' in accordance with the 
requirements of Sec.  1.824; and
    (ii) A statement that the sequence information contained in the CRF 
submitted under paragraph (e)(1)(i) of this section is identical to the 
sequence information contained in the ``Sequence Listing'' under 
paragraph (c) of this section.
    (2) If the ``Sequence Listing'' under paragraph (c) of this section 
in an application submitted under 35 U.S.C. 371 is a PDF file 
(paragraph (c)(2) of this section) or on physical sheets of paper 
(paragraph (c)(3) of this section), and not also as an ASCII plain text 
file, in compliance with Sec.  1.824 (paragraph (c)(1) of this 
section), then the following must be submitted:
    (i) A CRF of the ``Sequence Listing,'' in accordance with the 
requirements of Sec.  1.824; and
    (ii) A statement that the sequence information contained in the CRF 
submitted under paragraph (e)(2)(i) of this section is identical to the 
sequence information contained in the ``Sequence Listing'' under 
paragraph (c)(2) or (3) of this section.
    (3) If a ``Sequence Listing'' in ASCII plain text format, in 
compliance with Sec.  1.824, has not been submitted for an 
international application under the PCT, and that application contains 
disclosures of nucleotide and/or amino acid sequences, as defined in 
paragraph (a) of this section, and is to be searched by the United 
States International Searching Authority or examined by the United 
States International Preliminary Examining Authority, then the 
following must be submitted:
    (i) A CRF of the ``Sequence Listing,'' in accordance with the 
requirements of Sec.  1.824;
    (ii) The late furnishing fee for providing a ``Sequence Listing'' 
in response to an invitation, as set forth in Sec.  1.445(a)(5); and
    (iii) A statement that the sequence information contained in the 
CRF, submitted under paragraph (e)(3)(i) of this section, does not go 
beyond the disclosure in the international application as filed, or a 
statement that the information recorded in the ASCII plain text file, 
submitted under paragraph (e)(3)(i) of this section, is identical to 
the sequence listing contained in the international application as 
filed, as applicable.
    (4) The CRF may not be retained as a part of the patent application 
file.
* * * * *
    (g) If any of the requirements of paragraphs (b) through (e) of 
this section are not satisfied at the time of filing under 35 U.S.C. 
111(a) or at the time of entering the national stage under 35 U.S.C. 
371, the applicant will be notified and given a period of time within 
which to comply with such requirements in order to prevent abandonment 
of the application. Any amendment to add or replace a ``Sequence 
Listing'' and CRF copy thereof in reply to a requirement under

[[Page 57050]]

this paragraph must be submitted in accordance with the requirements of 
Sec.  1.825.
    (h) If any of the requirements of paragraph (e)(3) of this section 
are not satisfied at the time of filing an international application 
under the PCT, and the application is to be searched by the United 
States International Searching Authority or examined by the United 
States International Preliminary Examining Authority, the applicant may 
be sent a notice necessitating compliance with the requirements within 
a prescribed time period. Where a ``Sequence Listing'' under PCT Rule 
13ter is provided in reply to a requirement under this paragraph, it 
must be accompanied by a statement that the information recorded in the 
ASCII plain text file under paragraph (e)(3)(i) of this section is 
identical to the sequence listing contained in the international 
application as filed, or does not go beyond the disclosure in the 
international application as filed, as applicable. It must also be 
accompanied by the late furnishing fee, as set forth in Sec.  
1.445(a)(5). If the applicant fails to timely provide the required CRF, 
the United States International Searching Authority shall search only 
to the extent that a meaningful search can be performed without the 
CRF, and the United States International Preliminary Examining 
Authority shall examine only to the extent that a meaningful 
examination can be performed without the CRF.

0
11. Amend Sec.  1.822 by:
0
a. Revising paragraphs (b) and (c)(1), (3), (5) and (6);
0
b. Adding note 2 to paragraph (c);
0
c. Revising paragraphs (d)(1) and (3) through (5);
0
d. Adding note 3 to paragraph (d); and
0
e. Revising paragraph (e).
    The revisions and additions read as follows:


Sec.  1.822   Symbols and format to be used for nucleotide and/or amino 
acid sequence data.

* * * * *
    (b) The code for representing the nucleotide and/or amino acid 
sequence characters shall conform to the code set forth in appendices A 
and C to this subpart. No code other than that specified in these 
sections shall be used in nucleotide and amino acid sequences. A 
modified base or modified or unusual amino acid may be presented in a 
given sequence as the corresponding unmodified base or amino acid if 
the modified base or modified or unusual amino acid is one of those 
listed in appendices B and D to this subpart, and the modification is 
also set forth in the Feature section. Otherwise, each occurrence of a 
base or amino acid not appearing in appendices A and C, shall be listed 
in a given sequence as ``n'' or ``Xaa,'' respectively, with further 
information, as appropriate, given in the Feature section, by including 
one or more feature keys listed in appendices E and F to this subpart.

    Note 1 to paragraph (b):  Appendices A through F to this subpart 
contain Tables 1-6 of the World Intellectual Property Organization 
(WIPO) Handbook on Industrial Property Information and 
Documentation, Standard ST.25: Standard for the Presentation of 
Nucleotide and Amino Acid Sequence Listings in Patent Applications 
(2009).

    (c) * * *
    (1) A nucleotide sequence shall be listed using the lowercase 
letter for representing the one-letter code for the nucleotide bases 
set forth in appendix A to this subpart.
* * * * *
    (3) The bases in the coding parts of a nucleotide sequence shall be 
listed as triplets (codons). The amino acids corresponding to the 
codons in the coding parts of a nucleotide sequence shall be listed 
immediately below the corresponding codons. Where a codon spans an 
intron, the amino acid symbol shall be listed below the portion of the 
codon containing two nucleotides.
* * * * *
    (5) A nucleotide sequence shall be represented, only by a single 
strand, in the 5 to 3 direction, from left to right.
    (6) The enumeration of nucleotide bases shall start at the first 
base of the sequence with number 1. The enumeration shall be continuous 
through the whole sequence in the direction 5 to 3. The enumeration 
shall appear in the right margin, next to the line containing the one-
letter codes for the bases and giving the number of the last base of 
that line.
* * * * *

    Note 2 to paragraph (c):  Appendices A through F to this subpart 
contain Tables 1-6 of the World Intellectual Property Organization 
(WIPO) Handbook on Industrial Property Information and 
Documentation, Standard ST.25: Standard for the Presentation of 
Nucleotide and Amino Acid Sequence Listings in Patent Applications 
(2009).

    (d) * * *
    (1) The amino acids in a protein or peptide sequence shall be 
listed using the three-letter abbreviation, with the first letter as an 
uppercase character, as in Appendix C to this subpart.
* * * * *
    (3) An amino acid sequence shall be represented in the amino to 
carboxy direction, from left to right, and the amino and carboxy groups 
shall not be represented in the sequence.
    (4) The enumeration of amino acids may start at the first amino 
acid of the first mature protein, with the number 1. When represented, 
the amino acids preceding the mature protein (e.g., pre-sequences, pro-
sequences, pre-pro-sequences, and signal sequences) shall have negative 
numbers, counting backwards starting with the amino acid next to number 
1. Otherwise, the enumeration of amino acids shall start at the first 
amino acid at the amino terminal as number 1, and shall appear below 
every five amino acids of the sequence. The enumeration method for 
amino acid sequences that is set forth in this section remains 
applicable for amino acid sequences that are circular in configuration, 
with the exception that the designation of the first amino acid of the 
sequence may be made at the option of the applicant.
    (5) An amino acid sequence that contains internal terminator 
symbols (e.g., ``Ter,'' ``*,'' or ``.,'' etc.) may not be represented 
as a single amino acid sequence but shall be represented as separate 
amino acid sequences.

    Note 3 to paragraph (d):  Appendices A through F to this subpart 
contain Tables 1-6 of the World Intellectual Property Organization 
(WIPO) Handbook on Industrial Property Information and 
Documentation, Standard ST.25: Standard for the Presentation of 
Nucleotide and Amino Acid Sequence Listings in Patent Applications 
(2009).

    (e) A sequence with a gap or gaps shall be represented as a 
plurality of separate sequences, with separate sequence identifiers 
(Sec.  1.823(a)(5)), with the number of separate sequences being equal 
in number to the number of continuous strings of sequence data. A 
sequence composed of one or more noncontiguous segments of a larger 
sequence or segments from different sequences shall be presented as a 
separate sequence.

0
12. Revise Sec.  1.823 to read as follows:


Sec.  1.823   Requirements for content of a ``Sequence Listing'' part 
of the specification.

    (a) The ``Sequence Listing'' must comply with the following:
    (1) The order and presentation of the items of information in the 
``Sequence Listing'' shall conform to the arrangement in appendix G to 
this subpart. The submission of those items of information designated 
with an ``M'' is mandatory. The submission of those items of 
information designated with an ``O'' is optional.
    (2) Each item of information shall begin on a new line, with the 
numeric

[[Page 57051]]

identifier enclosed in angle brackets, as shown in appendix G to this 
subpart.
    (3) Set forth numeric identifiers <110> through <170> at the 
beginning of the ``Sequence Listing.''
    (4) Include each disclosed nucleotide and/or amino acid sequence, 
as defined in Sec.  1.821(a).
    (5) Assign a separate sequence identifier to each sequence, 
beginning with 1 and increasing sequentially by integers, and include 
the sequence identifier in numeric identifier <210>.
    (6) Use the code ``000'' in place of the sequence where no sequence 
is present for a sequence identifier.
    (7) Include the total number of SEQ ID NOs in numeric identifier 
<160>, as defined in appendix G to this subpart, whether followed by a 
sequence or by the code ``000.''
    (8) Must not contain more than 74 characters per line.
    (b)(1) Unless paragraph (b)(2) of this section applies, if the 
``Sequence Listing'' required by Sec.  1.821(c) is submitted as an 
ASCII plain text file via the USPTO patent electronic filing system or 
on a read-only optical disc, in compliance with Sec.  1.52(e), then the 
specification must contain a statement in a separate paragraph (see 
Sec.  1.77(b)(5)) that incorporates by reference the material in the 
ASCII plain text file identifying:
    (i) The name of the file;
    (ii) The date of creation; and
    (iii) The size of the file in bytes.
    (2) If the ``Sequence Listing'' required by Sec.  1.821(c) is 
submitted as an ASCII plain text file via the USPTO patent electronic 
filing system or on a read-only optical disc, in compliance with Sec.  
1.52(e) for an international application during the international 
stage, then incorporation by reference of the material in the ASCII 
plain text file is not required.
    (3) A ``Sequence Listing'' required by Sec.  1.821(c) that is 
submitted as a PDF file (Sec.  1.821(c)(2)) via the USPTO patent 
electronic filing system or on physical sheets of paper (Sec.  
1.821(c)(3)), setting forth the nucleotide and/or amino acid sequence 
and associated information in accordance with paragraph (a) of this 
section:
    (i) Must begin on a new page;
    (ii) Must be titled ``Sequence Listing'';
    (iii) Must not include material other than the ``Sequence Listing'' 
itself;
    (iv) Must have sheets containing no more than 66 lines, with each 
line containing no more than 74 characters;
    (v) Should have sheets numbered independently of the numbering of 
the remainder of the application; and
    (vi) Should use a fixed-width font exclusively throughout.

0
13. Revise Sec.  1.824 to read as follows:


Sec.  1.824   Form and format for a nucleotide and/or amino acid 
sequence submission as an ASCII plain text file.

    (a) A ``Sequence Listing'' under Sec.  1.821(c)(1) and the CRF 
required by Sec.  1.821(e) submitted as an ASCII plain text file may be 
created by any means, such as text editors, nucleotide/amino acid 
sequence editors, or other custom computer programs; however, the ASCII 
plain text file must conform to the following requirements:
    (1) Must have the following compatibilities:
    (i) Computer compatibility: PC or Mac[supreg]; and
    (ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg].
    (2) Must be in ASCII plain text, where:
    (i) All printable characters (including the space character) are 
permitted; and
    (ii) No nonprintable (ASCII control) characters are permitted, 
except ASCII CRLF or LF as line terminators.
    (3) Must be named as *.txt, where ``*'' is one character or a 
combination of characters limited to upper- or lowercase letters, 
numbers, hyphens, and underscores and does not exceed 60 characters in 
total, excluding the extension. No spaces or other types of characters 
are permitted in the file name.
    (4) Must contain no more than 74 printable characters in each line.
    (5) Pagination is not permitted; the ASCII plain text file must be 
one continuous file, with no ``hard page break'' codes and no page 
numbering.
    (b) The ASCII plain text file must contain a copy of a single 
``Sequence Listing'' in a single file and be submitted either:
    (1) Electronically via the USPTO patent electronic filing system, 
where the file must not exceed 100 MB, and file compression is not 
permitted; or
    (2) On a read-only optical disc(s), in compliance with Sec.  
1.52(e), where:
    (i) A file that is not compressed must be contained on a single 
read-only optical disc;
    (ii) The file may be compressed using WinZip[supreg], 7-Zip, or 
Unix[supreg]/Linux[supreg] Zip;
    (iii) A compressed file must not be self-extracting; and
    (iv) A compressed ASCII plain text file that does not fit on a 
single read-only optical disc may be split into multiple file parts, in 
accordance with the target read-only optical disc size, and labeled in 
compliance with Sec.  1.52(e)(5)(vi).

0
14. Revise Sec.  1.825 to read as follows:


Sec.  1.825   Amendment to add or replace a ``Sequence Listing'' and 
CRF copy thereof.

    (a) Any amendment adding a ``Sequence Listing'' (Sec.  1.821(c)) 
after the application filing date must include:
    (1) A ``Sequence Listing,'' in accordance with the requirements of 
Sec. Sec.  1.821 through 1.824, submitted as:
    (i) An ASCII plain text file, under Sec.  1.821(c)(1), via the 
USPTO patent electronic filing system or on a read-only optical disc, 
in compliance with Sec.  1.52(e);
    (ii) A PDF file via the USPTO patent electronic filing system; or
    (iii) Physical sheets of paper;
    (2) A request that the amendment be made:
    (i) By incorporation by reference of the material in the ASCII 
plain text file, in a separate paragraph of the specification, 
identifying the name of the file, the date of creation, and the size of 
the file in bytes (see Sec.  1.77(b)(5)), for a ``Sequence Listing'' 
submitted under Sec.  1.821(c)(1), except when submitted to the United 
States International Preliminary Examining Authority for an 
international application; or
    (ii) By inserting, after the abstract of the disclosure, a 
``Sequence Listing'' submitted as a PDF file under Sec.  1.821(c)(2) or 
submitted on physical sheets of paper under Sec.  1.821(c)(3), except 
when submitted to the United States International Preliminary Examining 
Authority for an international application;
    (3) A statement that indicates the basis for the amendment, with 
specific references to particular parts of the application 
(specification, claims, drawings) for all sequence data in the 
``Sequence Listing'' in the application as originally filed;
    (4) A statement that the ``Sequence Listing'' includes no new 
matter;
    (5) A new or substitute CRF under Sec.  1.821(e), if:
    (i) The added ``Sequence Listing'' is submitted as a PDF file, 
under Sec.  1.821(c)(2), or on physical sheets of paper, under Sec.  
1.821(c)(3); and
    (ii) A CRF, under Sec.  1.821(e), was not submitted, not compliant 
with Sec.  1.824, or not the same as the ``Sequence Listing''; and
    (6) A statement that the sequence information contained in the CRF 
is the same as the sequence information contained in the added 
``Sequence Listing,'' if submitted as a PDF file, under Sec.  
1.821(c)(2), or on physical sheets of paper, under Sec.  1.821(c)(3).
    (b) Any amendment to a ``Sequence Listing'' (Sec.  1.821(c)) must 
include:
    (1) A replacement ``Sequence Listing,'' in accordance with the 
requirements of Sec. Sec.  1.821 through 1.824, submitted as:

[[Page 57052]]

    (i) An ASCII plain text file, under Sec.  1.821(c)(1), via the 
USPTO patent electronic filing system, or on a read-only optical disc, 
in compliance with Sec.  1.52(e), labeled as ``REPLACEMENT MM/DD/YYYY'' 
(with the month, day, and year of creation indicated);
    (ii) A PDF file via the USPTO patent electronic filing system; or
    (iii) Physical sheets of paper;
    (2) A request that the amendment be made:
    (i) By incorporation by reference of the material in the ASCII 
plain text file, in a separate paragraph of the specification 
(replacing any prior such paragraph, as applicable) identifying the 
name of the file, the date of creation, and the size of the file in 
bytes (see Sec.  1.77(b)(5)) for a ``Sequence Listing'' under Sec.  
1.821(c)(1), except when submitted to the United States International 
Preliminary Examining Authority for an international application; or
    (ii) By placing, after the abstract of the disclosure, a ``Sequence 
Listing'' submitted as a PDF file, under Sec.  1.821(c)(2), or on 
physical sheets of paper, under Sec.  1.821(c)(3) (replacing any prior 
``Sequence Listing,'' as applicable), except when submitted to the 
United States International Preliminary Examining Authority for an 
international application;
    (3) A statement that identifies the location of all deletions, 
replacements, or additions to the ``Sequence Listing'';
    (4) A statement that indicates the basis for the amendment, with 
specific references to particular parts of the application 
(specification, claims, drawings) as originally filed for all amended 
sequence data in the replacement ``Sequence Listing'';
    (5) A statement that the replacement ``Sequence Listing'' includes 
no new matter;
    (6) A new or substitute CRF, under Sec.  1.821(e), with the 
amendment incorporated therein, if:
    (i) The replacement ``Sequence Listing'' is submitted as a PDF 
file, under Sec.  1.821(c)(2), or on physical sheets of paper, under 
Sec.  1.821(c)(3); and
    (ii) A CRF, under Sec.  1.821(e), was not submitted, not compliant 
with Sec.  1.824, or not the same as the submitted ``Sequence 
Listing''; and
    (7) A statement that the sequence information contained in the CRF 
is the same as the sequence information contained in the replacement 
``Sequence Listing'' when submitted as a PDF file, under Sec.  
1.821(c)(2), or on physical sheets of paper, under Sec.  1.821(c)(3).
    (c) The specification of a complete application, filed on the 
application filing date, with a ``Sequence Listing'' as an ASCII plain 
text file, under Sec.  1.821(c)(1), without an incorporation by 
reference of the material contained in the ASCII plain text file, must 
be amended to contain a separate paragraph incorporating by reference 
the material contained in the ASCII plain text file, in accordance with 
Sec.  1.77(b)(5), except for international applications during the 
international stage or national stage.
    (d) Any appropriate amendments to the ``Sequence Listing'' in a 
patent (e.g., by reason of reissue, reexamination, or a certificate of 
correction) must comply with the requirements of paragraph (b) of this 
section.

0
15. Redesignate appendix A to subpart G of part 1 as appendix G to 
subpart G, add appendices A through F to subpart G, and revise the 
newly redesignated appendix G to read as follows:

Sec.
* * * * *
Appendix A to Subpart G of Part 1--List of Nucleotides
Appendix B to Subpart G of Part 1--List of Modified Nucleotides
Appendix C to Subpart G of Part 1--List of Amino Acids
Appendix D to Subpart G of Part 1--List of Modified and Unusual 
Amino Acids
Appendix E to Subpart G of Part 1--List of Feature Keys Related to 
Nucleotide Sequences
Appendix F to Subpart G of Part 1--List of Feature Keys Related to 
Protein Sequences
Appendix G to Subpart G of Part 1--Numeric Identifiers

Appendix A to Subpart G of Part 1--List of Nucleotides

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009).

------------------------------------------------------------------------
                                                           Origin of
             Symbol                     Meaning           designation
------------------------------------------------------------------------
A...............................  a.................  Adenine.
G...............................  g.................  Guanine.
C...............................  c.................  Cytosine.
T...............................  t.................  Thymine.
U...............................  u.................  Uracil.
r...............................  g or a............  Purine.
y...............................  t/u or c..........  Pyrimidine.
m...............................  a or c............  Amino.
k...............................  g or t/u..........  Keto.
s...............................  g or c............  strong
                                                       interactions 3H-
                                                       bonds.
w...............................  a or t/u..........  weak interactions
                                                       2H-bonds.
b...............................  g or c or t/u.....  not a.
d...............................  a or g or t/u.....  not c.
h...............................  a or c or t/u.....  not g.
v...............................  a or g or c.......  not t, not u.
n...............................  a or g or c or t/   Any.
                                   u, unknown, or
                                   other.
------------------------------------------------------------------------

Appendix B to Subpart G of Part 1--List of Modified Nucleotides

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009).

------------------------------------------------------------------------
              Symbol                               Meaning
------------------------------------------------------------------------
ac4c..............................  4-acetylcytidine.
chm5u.............................  5-(carboxyhydroxymethyl)uridine.

[[Page 57053]]

 
cm................................  2'-O-methylcytidine.
cmnm5s2u..........................  5-carboxymethylaminomethyl-2-
                                     thiouridine.
cmnm5u............................  5-carboxymethylaminomethyluridine.
d.................................  Dihydrouridine.
fm................................  2'-O-methylpseudouridine.
gal q.............................  beta, D-galactosylqueuosine.
gm................................  2'-O-methylguanosine.
i.................................  Inosine.
i6a...............................  N6-isopentenyladenosine.
m1a...............................  1-methyladenosine.
m1f...............................  1-methylpseudouridine.
m1g...............................  1-methylguanosine.
m1i...............................  1-methylinosine.
m22g..............................  2,2-dimethylguanosine.
m2a...............................  2-methyladenosine.
m2g...............................  2-methylguanosine.
m3c...............................  3-methylcytidine.
m5c...............................  5-methylcytidine.
m6a...............................  N6-methyladenosine.
m7g...............................  7-methylguanosine.
mam5u.............................  5-methylaminomethyluridine.
mam5s2u...........................  5-methoxyaminomethyl-2-thiouridine.
man q.............................  beta, D-mannosylqueuosine.
mcm5s2u...........................  5-methoxycarbonylmethyl-2-
                                     thiouridine.
mcm5u.............................  5-methoxycarbonylmethyluridine.
mo5u..............................  5-methoxyuridine.
ms2i6a............................  2-methylthio-N6-
                                     isopentenyladenosine.
ms2t6a............................  N-((9-beta-D-ribofuranosyl-2-
                                     methylthiopurine-6-
                                     yl)carbamoyl)threonine.
mt6a..............................  N-((9-beta-D-ribofuranosylpurine-6-
                                     yl)N-methylcarbamoyl)threonine.
mv................................  uridine-5-oxyacetic acid-
                                     methylester.
o5u...............................  uridine-5-oxyacetic acid.
osyw..............................  Wybutoxosine.
p.................................  Pseudouridine.
q.................................  Queuosine.
s2c...............................  2-thiocytidine.
s2t...............................  5-methyl-2-thiouridine.
s2u...............................  2-thiouridine.
s4u...............................  4-thiouridine.
t.................................  5-methyluridine.
t6a...............................  N-((9-beta-D-ribofuranosylpurine-6-
                                     yl)-carbamoyl)threonine.
tm................................  2'-O-methyl-5-methyluridine.
um................................  2'-O-methyluridine.
yw................................  Wybutosine.
x.................................  3-(3-amino-3-carboxy-propyl)uridine,
                                     (acp3)u.
------------------------------------------------------------------------

Appendix C to Subpart G of Part 1--List of Amino Acids

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009).

------------------------------------------------------------------------
              Symbol                               Meaning
------------------------------------------------------------------------
Ala...............................  Alanine.
Cys...............................  Cysteine.
Asp...............................  Aspartic Acid.
Glu...............................  Glutamic Acid.
Phe...............................  Phenylalanine.
Gly...............................  Glycine.
His...............................  Histidine.
Ile...............................  Isoleucine.
Lys...............................  Lysine.
Leu...............................  Leucine.
Met...............................  Methionine.
Asn...............................  Asparagine.
Pro...............................  Proline.
Gln...............................  Glutamine.
Arg...............................  Arginine.
Ser...............................  Serine.
Thr...............................  Threonine.
Val...............................  Valine.
Trp...............................  Tryptophan.

[[Page 57054]]

 
Tyr...............................  Tyrosine.
Asx...............................  Asp or Asn.
Glx...............................  Glu or Gln.
Xaa...............................  unknown or other.
------------------------------------------------------------------------

Appendix D to Subpart G of Part 1--List of Modified and Unusual Amino 
Acids

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009).

------------------------------------------------------------------------
              Symbol                               Meaning
------------------------------------------------------------------------
Aad...............................  2-Aminoadipic acid.
bAad..............................  3-Aminoadipic acid.
bAla..............................  beta-Alanine, beta-Aminopropionic
                                     acid.
Abu...............................  2-Aminobutyric acid.
4Abu..............................  4-Aminobutyric acid, piperidinic
                                     acid.
Acp...............................  6-Aminocaproic acid.
Ahe...............................  2-Aminoheptanoic acid.
Aib...............................  2-Aminoisobutyric acid.
bAib..............................  3-Aminoisobutyric acid.
Apm...............................  2-Aminopimelic acid.
Dbu...............................  2,4 Diaminobutyric acid.
Des...............................  Desmosine.
Dpm...............................  2,2'-Diaminopimelic acid.
Dpr...............................  2,3-Diaminopropionic acid.
EtGly.............................  N-Ethylglycine.
EtAsn.............................  N-Ethylasparagine.
Hyl...............................  Hydroxylysine.
aHyl..............................  allo-Hydroxylysine.
3Hyp..............................  3-Hydroxyproline.
4Hyp..............................  4-Hydroxyproline.
Ide...............................  Isodesmosine.
aIle..............................  allo-Isoleucine.
MeGly.............................  N-Methylglycine, sarcosine.
MeIle.............................  N-Methylisoleucine.
MeLys.............................  6-N-Methyllysine.
MeVal.............................  N-Methylvaline.
Nva...............................  Norvaline.
Nle...............................  Norleucine.
Orn...............................  Ornithine.
------------------------------------------------------------------------

Appendix E to Subpart G of Part 1--List of Feature Keys Related to 
Nucleotide Sequences

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009).

------------------------------------------------------------------------
            Key                              Description
------------------------------------------------------------------------
allele.....................  a related individual or strain contains
                              stable, alternative forms of the same
                              gene, which differs from the presented
                              sequence at this location (and perhaps
                              others).
attenuator.................  (1) region of DNA at which regulation of
                              termination of transcription occurs, which
                              controls the expression of some bacterial
                              operons; (2) sequence segment located
                              between the promoter and the first
                              structural gene that causes partial
                              termination of transcription.
C_region...................  constant region of immunoglobulin light and
                              heavy chains, and T-cell receptor alpha,
                              beta, and gamma chains; includes one or
                              more exons depending on the particular
                              chain.
CAAT_signal................  CAAT box; part of a conserved sequence
                              located about 75 bp upstream of the start
                              point of eukaryotic transcription units
                              which may be involved in RNA polymerase
                              binding; consensus=GG (C or T) CAATCT.
CDS........................  coding sequence; sequence of nucleotides
                              that corresponds with the sequence of
                              amino acids in a protein (location
                              includes stop codon); feature includes
                              amino acid conceptual translation.
conflict...................  independent determinations of the ``same''
                              sequence differ at this site or region.
D-loop.....................  displacement loop; a region within
                              mitochondrial DNA in which a short stretch
                              of RNA is paired with one strand of DNA,
                              displacing the original partner DNA strand
                              in this region; also used to describe the
                              displacement of a region of one strand of
                              duplex DNA by a single stranded invader in
                              the reaction catalyzed by RecA protein.
D-segment..................  diversity segment of immunoglobulin heavy
                              chain, and T-cell receptor beta chain.

[[Page 57055]]

 
enhancer...................  a cis-acting sequence that increases the
                              utilization of (some) eukaryotic
                              promoters, and can function in either
                              orientation and in any location (upstream
                              or downstream) relative to the promoter.
exon.......................  region of genome that codes for portion of
                              spliced mRNA; may contain 5'UTR, all CDSs,
                              and 3'UTR.
GC_signal..................  GC box; a conserved GC-rich region located
                              upstream of the start point of eukaryotic
                              transcription units which may occur in
                              multiple copies or in either orientation;
                              consensus=GGGCGG.
gene.......................  region of biological interest identified as
                              a gene and for which a name has been
                              assigned.
iDNA.......................  intervening DNA; DNA which is eliminated
                              through any of several kinds of
                              recombination.
intron.....................  a segment of DNA that is transcribed, but
                              removed from within the transcript by
                              splicing together the sequences (exons) on
                              either side of it.
J_segment..................  joining segment of immunoglobulin light and
                              heavy chains, and T-cell receptor alpha,
                              beta, and gamma chains.
LTR........................  long terminal repeat, a sequence directly
                              repeated at both ends of a defined
                              sequence, of the sort typically found in
                              retroviruses.
mat_peptide................  mature peptide or protein coding sequence;
                              coding sequence for the mature or final
                              peptide or protein product following post-
                              translational modification; the location
                              does not include the stop codon (unlike
                              the corresponding CDS).
misc_binding...............  site in nucleic acid which covalently or
                              non-covalently binds another moiety that
                              cannot be described by any other Binding
                              key (primer_bind or protein_bind).
misc_difference............  feature sequence is different from that
                              presented in the entry and cannot be
                              described by any other Difference key
                              (conflict, unsure, old_sequence, mutation,
                              variation, allele, or modified_base).
misc_feature...............  region of biological interest which cannot
                              be described by any other feature key; a
                              new or rare feature.
misc_recomb................  site of any generalized, site-specific or
                              replicative recombination event where
                              there is a breakage and reunion of duplex
                              DNA that cannot be described by other
                              recombination keys (iDNA and virion) or
                              qualifiers of source key (/insertion_seq,
                              transposon, /proviral).
misc_RNA...................  any transcript or RNA product that cannot
                              be defined by other RNA keys
                              (prim_transcript, precursor_RNA, mRNA,
                              5'clip, 3'clip, 5'UTR, 3'UTR, exon, CDS,
                              sig_peptide, transit_peptide, mat_peptide,
                              intron, polyA_site, rRNA, tRNA, scRNA, and
                              snRNA).
misc_signal................  any region containing a signal controlling
                              or altering gene function or expression
                              that cannot be described by other Signal
                              keys (promoter, CAAT_signal, TATA_signal,
                              35_signal, -10_signal, GC_signal, RBS,
                              polyA_signal, enhancer, attenuator,
                              terminator, and rep_origin).
misc_structure.............  any secondary or tertiary structure or
                              conformation that cannot be described by
                              other Structure keys (stem_loop and D-
                              loop).
modified_base..............  the indicated nucleotide is a modified
                              nucleotide and should be substituted for
                              by the indicated molecule (given in the
                              mod_base qualifier value).
mRNA.......................  messenger RNA; includes 5' untranslated
                              region (5'UTR), coding sequences (CDS,
                              exon) and 3' untranslated region (3'UTR).
mutation...................  a related strain has an abrupt, inheritable
                              change in the sequence at this location.
N_region...................  extra nucleotides inserted between
                              rearranged immunoglobulin segments.
old_sequence...............  the presented sequence revises a previous
                              version of the sequence at this location.
polyA_signal...............  recognition region necessary for
                              endonuclease cleavage of an RNA transcript
                              that is followed by polyadenylation;
                              consensus=AATAAA.
polyA_site.................  site on an RNA transcript to which will be
                              added adenine residues by post-
                              transcriptional polyadenylation.
precursor_RNA..............  any RNA species that is not yet the mature
                              RNA product; may include 5' clipped region
                              (5'clip), 5' untranslated region (5'UTR),
                              coding sequences (CDS, exon), intervening
                              sequences (intron), 3' untranslated region
                              (3'UTR), and 3' clipped region (3'clip).
prim_transcript............  primary (initial, unprocessed) transcript;
                              includes 5' clipped region (5'clip), 5'
                              untranslated region (5'UTR), coding
                              sequences (CDS, exon), intervening
                              sequences (intron), 3' untranslated region
                              (3'UTR), and 3' clipped region (3'clip).
primer_bind................  non-covalent primer binding site for
                              initiation of replication, transcription,
                              or reverse transcription; includes site(s)
                              for synthetic, for example, PCR primer
                              elements.
promoter...................  region on a DNA molecule involved in RNA
                              polymerase binding to initiate
                              transcription.
protein_bind...............  non-covalent protein binding site on
                              nucleic acid.
RBS........................  ribosome binding site.
repeat_region..............  region of genome containing repeating
                              units.
repeat_unit................  single repeat element.
rep_origin.................  origin of replication; starting site for
                              duplication of nucleic acid to give two
                              identical copies.
rRNA.......................  mature ribosomal RNA; the RNA component of
                              the ribonucleoprotein particle (ribosome)
                              which assembles amino acids into proteins.
S_region...................  switch region of immunoglobulin heavy
                              chains; involved in the rearrangement of
                              heavy chain DNA leading to the expression
                              of a different immunoglobulin class from
                              the same B-cell.
satellite..................  many tandem repeats (identical or related)
                              of a short basic repeating unit; many have
                              a base composition or other property
                              different from the genome average that
                              allows them to be separated from the bulk
                              (main band) genomic DNA.
scRNA......................  small cytoplasmic RNA; any one of several
                              small cytoplasmic RNA molecules present in
                              the cytoplasm and (sometimes) nucleus of a
                              eukaryote.
sig_peptide................  signal peptide coding sequence; coding
                              sequence for an N-terminal domain of a
                              secreted protein; this domain is involved
                              in attaching nascent polypeptide to the
                              membrane; leader sequence.
snRNA......................  small nuclear RNA; any one of many small
                              RNA species confined to the nucleus;
                              several of the snRNAs are involved in
                              splicing or other RNA processing
                              reactions.
source.....................  identifies the biological source of the
                              specified span of the sequence; this key
                              is mandatory; every entry will have, as a
                              minimum, a single source key spanning the
                              entire sequence; more than one source key
                              per sequence is permissible.
stem_loop..................  hairpin; a double-helical region formed by
                              base-pairing between adjacent (inverted)
                              complementary sequences in a single strand
                              of RNA or DNA.
STS........................  Sequence Tagged Site; short, single-copy
                              DNA sequence that characterizes a mapping
                              landmark on the genome and can be detected
                              by PCR; a region of the genome can be
                              mapped by determining the order of a
                              series of STSs.
TATA_signal................  TATA box; Goldberg-Hogness box; a conserved
                              AT-rich septamer found about 25 bp before
                              the start point of each eukaryotic RNA
                              polymerase II transcript unit which may be
                              involved in positioning the enzyme for
                              correct initiation; consensus=TATA(A or
                              T)A(A or T).

[[Page 57056]]

 
terminator.................  sequence of DNA located either at the end
                              of the transcript or adjacent to a
                              promoter region that causes RNA polymerase
                              to terminate transcription; may also be
                              site of binding of repressor protein.
transit_peptide............  transit peptide coding sequence; coding
                              sequence for an N-terminal domain of a
                              nuclear-encoded organellar protein; this
                              domain is involved in post-translational
                              import of the protein into the organelle.
tRNA.......................  mature transfer RNA, a small RNA molecule
                              (75-85 bases long) that mediates the
                              translation of a nucleic acid sequence
                              into an amino acid sequence.
unsure.....................  author is unsure of exact sequence in this
                              region.
V_region...................  variable region of immunoglobulin light and
                              heavy chains, and T-cell receptor alpha,
                              beta, and gamma chains; codes for the
                              variable amino terminal portion; can be
                              made up from V_segments, D_segments,
                              N_regions, and J_segments.
V_segment..................  variable segment of immunoglobulin light
                              and heavy chains, and T-cell receptor
                              alpha, beta, and gamma chains; codes for
                              most of the variable region (V_region) and
                              the last few amino acids of the leader
                              peptide.
variation..................  a related strain contains stable mutations
                              from the same gene (for example, RFLPs,
                              polymorphisms, etc.) which differ from the
                              presented sequence at this location (and
                              possibly others).
3'clip.....................  3'-most region of a precursor transcript
                              that is clipped off during processing.
3'UTR......................  region at the 3' end of a mature transcript
                              (following the stop codon) that is not
                              translated into a protein.
5'clip.....................  5'-most region of a precursor transcript
                              that is clipped off during processing.
5'UTR......................  region at the 5' end of a mature transcript
                              (preceding the initiation codon) that is
                              not translated into a protein.
-10_signal.................  pribnow box; a conserved region about 10 bp
                              upstream of the start point of bacterial
                              transcription units which may be involved
                              in binding RNA polymerase;
                              consensus=TAtAaT.
-35_signal.................  a conserved hexamer about 35 bp upstream of
                              the start point of bacterial transcription
                              units; consensus=TTGACa [ ] or TGTTGACA [
                              ].
------------------------------------------------------------------------

Appendix F to Subpart G of Part 1--List of Feature Keys Related to 
Protein Sequences

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009).

------------------------------------------------------------------------
             Key                              Description
------------------------------------------------------------------------
CONFLICT.....................  different papers report differing
                                sequences.
VARIANT......................  authors report that sequence variants
                                exist.
VARSPLIC.....................  description of sequence variants produced
                                by alternative splicing.
MUTAGEN......................  site which has been experimentally
                                altered.
MOD_RES......................  post-translational modification of a
                                residue.
ACETYLATION..................  N-terminal or other.
AMIDATION....................  generally at the C-terminal of a mature
                                active peptide.
BLOCKED......................  undetermined N- or C-terminal blocking
                                group.
FORMYLATION..................  of the N-terminal methionine.
GAMMA-CARBOXYGLUTAMIC ACID     of asparagine, aspartic acid, proline, or
 HYDROXYLATION.                 lysine.
METHYLATION..................  generally of lysine or arginine.
PHOSPHORYLATION..............  of serine, threonine, tyrosine, aspartic
                                acid or histidine.
PYRROLIDONE CARBOXYLIC ACID..  N-terminal glutamate which has formed an
                                internal cyclic lactam.
SULFATATION..................  generally of tyrosine.
LIPID........................  covalent binding of a lipidic moiety.
MYRISTATE....................  myristate group attached through an amide
                                bond to the N-terminal glycine residue
                                of the mature form of a protein or to an
                                internal lysine residue.
PALMITATE....................  palmitate group attached through a
                                thioether bond to a cysteine residue or
                                through an ester bond to a serine or
                                threonine residue.
FARNESYL.....................  farnesyl group attached through a
                                thioether bond to a cysteine residue.
GERANYL-GERANYL..............  geranyl-geranyl group attached through a
                                thioether bond to a cysteine residue.
GPI-ANCHOR...................  glycosyl-phosphatidylinositol (GPI) group
                                linked to the alpha- carboxyl group of
                                the C-terminal residue of the mature
                                form of a protein.
N-ACYL DIGLYCERIDE...........  N-terminal cysteine of the mature form of
                                a prokaryotic lipoprotein with an amide-
                                linked fatty acid and a glyceryl group
                                to which two fatty acids are linked by
                                ester linkages.
DISULFID.....................  disulfide bond; the `FROM' and `TO'
                                endpoints represent the two residues
                                which are linked by an intra-chain
                                disulfide bond; if the `FROM' and `TO'
                                endpoints are identical, the disulfide
                                bond is an interchain one and the
                                description field indicates the nature
                                of the cross-link.
THIOLEST.....................  thiolester bond; the `FROM' and `TO'
                                endpoints represent the two residues
                                which are linked by the thiolester bond.
THIOETH......................  thioether bond; the `FROM' and `TO'
                                endpoints represent the two residues
                                which are linked by the thioether bond.
CARBOHYD.....................  glycosylation site; the nature of the
                                carbohydrate (if known) is given in the
                                description field.
METAL........................  binding site for a metal ion; the
                                description field indicates the nature
                                of the metal.
BINDING......................  binding site for any chemical group (co-
                                enzyme, prosthetic group, etc.); the
                                chemical nature of the group is given in
                                the description field.
SIGNAL.......................  extent of a signal sequence (prepeptide).
TRANSIT......................  extent of a transit peptide
                                (mitochondrial, chloroplastic, or for a
                                microbody).
PROPEP.......................  extent of a propeptide.
CHAIN........................  extent of a polypeptide chain in the
                                mature protein.

[[Page 57057]]

 
PEPTIDE......................  extent of a released active peptide.
DOMAIN.......................  extent of a domain of interest on the
                                sequence; the nature of that domain is
                                given in the description field.
CA_BIND......................  extent of a calcium-binding region.
DNA_BIND.....................  extent of a DNA-binding region.
NP_BIND......................  extent of a nucleotide phosphate binding
                                region; the nature of the nucleotide
                                phosphate is indicated in the
                                description field.
TRANSMEM.....................  extent of a transmembrane region.
ZN_FING......................  extent of a zinc finger region.
SIMILAR......................  extent of a similarity with another
                                protein sequence; precise information,
                                relative to that sequence, is given in
                                the description field.
REPEAT.......................  extent of an internal sequence
                                repetition.
HELIX........................  secondary structure: Helices, for
                                example, Alpha-helix, 3(10) helix, or Pi-
                                helix.
STRAND.......................  secondary structure: Beta-strand, for
                                example, Hydrogen bonded beta-strand, or
                                Residue in an isolated beta-bridge.
TURN.........................  secondary structure Turns, for example, H-
                                bonded turn (3-turn, 4-turn, or 5-turn).
ACT_SITE.....................  amino acid(s) involved in the activity of
                                an enzyme.
SITE.........................  any other interesting site on the
                                sequence.
INIT_MET.....................  the sequence is known to start with an
                                initiator methionine.
NON_TER......................  the residue at an extremity of the
                                sequence is not the terminal residue; if
                                applied to position 1, this signifies
                                that the first position is not the N-
                                terminus of the complete molecule; if
                                applied to the last position, it
                                signifies that this position is not the
                                C-terminus of the complete molecule;
                                there is no description field for this
                                key.
NON_CONS.....................  non consecutive residues; indicates that
                                two residues in a sequence are not
                                consecutive and that there are a number
                                of unsequenced residues between them.
UNSURE.......................  uncertainties in the sequence; used to
                                describe region(s) of a sequence for
                                which the authors are unsure about the
                                sequence assignment.
------------------------------------------------------------------------

Appendix G to Subpart G of Part 1--Numeric Identifiers

------------------------------------------------------------------------
                                          Comments and    Mandatory (M)
  Numeric identifier      Definition         format      or optional (O)
------------------------------------------------------------------------
<110>................  Applicant......  If Applicant is  M.
                                         inventor, then
                                         preferably
                                         max. of 10
                                         names; one
                                         name per line;
                                         preferable
                                         format:
                                         Surname, Other
                                         Names and/or
                                         Initials.
<120>................  Title of         ...............  M.
                        Invention.
<130>................  File Reference.  Personal file    M when filed
                                         reference.       prior to
                                                          assignment or
                                                          appl. number.
<140>................  Current          Specify as: US   M, if
                        Application      09/999,999 or    available.
                        Number.          PCT/US09/99999.
<141>................  Current Filing   Specify as:      M, if
                        Date.            yyyy-mm-dd.      available.
<150>................  Prior            Specify as: US   M, if
                        Application      09/999,999 or    applicable
                        Number.          PCT/US09/99999.  include
                                                          priority
                                                          documents
                                                          under 35
                                                          U.S.C. 119 and
                                                          120.
<151>................  Prior            Specify as:      M, if
                        Application      yyyy-mm-dd.      applicable.
                        Filing Date.
<160>................  Number of SEQ    Count includes   M.
                        ID NOs.          total number
                                         of SEQ ID NOs.
<170>................  Software.......  Name of          O.
                                         software used
                                         to create the
                                         ``Sequence
                                         Listing''.
<210>................  SEQ ID NO:#:...  Response shall   M.
                                         be an integer
                                         representing
                                         the SEQ ID NO
                                         shown.
<211>................  Length.........  Respond with an  M.
                                         integer
                                         expressing the
                                         number of
                                         bases or amino
                                         acid residues.
<212>................  Type...........  Whether          M.
                                         presented
                                         sequence
                                         molecule is
                                         DNA, RNA, or
                                         PRT (protein).
                                         If a
                                         nucleotide
                                         sequence
                                         contains both
                                         DNA and RNA
                                         fragments, the
                                         type shall be
                                         ``DNA.'' In
                                         addition, the
                                         combined DNA/
                                         RNA molecule
                                         shall be
                                         further
                                         described in
                                         the <220> to
                                         <223> feature
                                         section.
<213>................  Organism.......  Scientific       M.
                                         name, i.e.,
                                         Genus/species,
                                         Unknown or
                                         Artificial
                                         Sequence. In
                                         addition, the
                                         ``Unknown'' or
                                         ``Artificial
                                         Sequence''
                                         organisms
                                         shall be
                                         further
                                         described in
                                         the <220> to
                                         <223> feature
                                         section.
<220>................  Feature........  Leave blank      M, under the
                                         after <220>.     following
                                         <221-223>        conditions: If
                                         provide for a    ``n,''
                                         description of   ``Xaa,'' or a
                                         points of        modified or
                                         biological       unusual L-
                                         significance     amino acid or
                                         in the           modified base
                                         sequence.        was used in a
                                                          sequence; if
                                                          ORGANISM is
                                                          ``Artificial
                                                          Sequence'' or
                                                          ``Unknown'';
                                                          if molecule is
                                                          combined DNA/
                                                          RNA.

[[Page 57058]]

 
<221>................  Name/Key.......  Provide          M, under the
                                         appropriate      following
                                         identifier for   conditions: If
                                         feature, from    ``n,''
                                         WIPO Standard    ``Xaa,'' or a
                                         ST.25 (2009),    modified or
                                         Appendices E     unusual L-
                                         and F to this    amino acid or
                                         subpart.         modified base
                                                          was used in a
                                                          sequence.
<222>................  Location.......  Specify          M, under the
                                         location         following
                                         within           conditions: If
                                         sequence;        ``n,''
                                         where            ``Xaa,'' or a
                                         appropriate,     modified or
                                         state number     unusual L-
                                         of first and     amino acid or
                                         last bases/      modified base
                                         amino acids in   was used in a
                                         feature.         sequence.
<223>................  Other            Other relevant   M, under the
                        Information.     information;     following
                                         four lines       conditions: If
                                         maximum.         ``n,''
                                                          ``Xaa,'' or a
                                                          modified or
                                                          unusual L-
                                                          amino acid or
                                                          modified base
                                                          was used in a
                                                          sequence; if
                                                          ORGANISM is
                                                          ``Artificial
                                                          Sequence'' or
                                                          ``Unknown'';
                                                          if molecule is
                                                          combined DNA/
                                                          RNA.
<300>................  Publication      Leave blank      O.
                        Information.     after <30>.
<301>................  Authors........  Preferably max.  O.
                                         of 10 named
                                         authors of
                                         publication;
                                         specify one
                                         name per line;
                                         preferable
                                         format:
                                         Surname, Other
                                         Names and/or
                                         Initials.
<302>................  Title..........  ...............  O.
<303>................  Journal........  ...............  O.
<304>................  Volume.........  ...............  O.
<305>................  Issue..........  ...............  O.
<306>................  Pages..........  ...............  O.
<307>................  Date...........  Journal date on  O.
                                         which data
                                         published;
                                         specify as
                                         yyyy-mm-dd,
                                         MMM-yyyy or
                                         Season-yyyy.
<308>................  Database         Accession        O.
                        Accession        number
                        Number.          assigned by
                                         database,
                                         including
                                         database name.
<309>................  Database Entry   Date of entry    O.
                        Date.            in database;
                                         specify as
                                         yyyy-mm-dd or
                                         MMM-yyyy.
<310>................  Patent Document  Document         O.
                        Number.          number; for
                                         patent-type
                                         citations
                                         only. Specify
                                         as, for
                                         example, US 09/
                                         999,999.
<311>................  Patent Filing    Document filing  O.
                        Date.            date, for
                                         patent-type
                                         citations
                                         only; specify
                                         as yyyy-mm-dd.
<312>................  Publication      Document         O.
                        Date.            publication
                                         date, for
                                         patent-type
                                         citations
                                         only; specify
                                         as yyyy-mm-dd.
<313>................  Relevant         FROM (position)  O.
                        Residues.        TO (position).
<400>................  Sequence.......  SEQ ID NO        M.
                                         should follow
                                         the numeric
                                         identifier and
                                         should appear
                                         on the line
                                         preceding the
                                         actual
                                         sequence.
------------------------------------------------------------------------


Andrew Hirshfeld,
Commissioner for Patents, Performing the Functions and Duties of the 
Under Secretary of Commerce for Intellectual Property and Director of 
the United States Patent and Trademark Office.
[FR Doc. 2021-22217 Filed 10-13-21; 8:45 am]
BILLING CODE 3510-16-P