MPEP § 2417 — MPEP § 2417
Current through: 2022-07-01

2417-Helpful Hints for Sequence Rules Compliance under WIPO Standard ST.26 
 
 

 
 
 
 
 
 
 
 

 

 
 
 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
 
 
 
 

 
 
 
 
 
 
 
 
 
 
 

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 Chapter 2400 

 Section 2417 
 

 
 
 
 
 
 2417 Helpful Hints for Sequence Rules Compliance under
 WIPO Standard ST.26 [R-01.2024]
 

 [Editor Note: This section is applicable to all applications with a
 filing date, or, for national phase applications, an international filing date, on or
 after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid
 sequences as defined in 37 CFR
 1.831(b) .] 

 The Office has the following non-exhaustive tips regarding
 sequence rules in compliance with WIPO Standard ST.26, as incorporated by reference in
 37 CFR
 1.839 and implemented by 37 CFR
 1.831 - 1.835 . 
 

 —Compliance is not required for establishing a filing date. 

 ─ A sequence listing submitted with a new application in
 compliance with 37 CFR 1.831 - 1.834 is considered part of the
 specification and thus contributes to disclosure of the invention for the purpose of
 35 U.S.C.
 112 .
 

 —Compliance is not per se a new matter issue. See
 MPEP §
 2414.02 for adding initial sequence listings under
 37 CFR
 1.835(a)(2) - (4) and MPEP §
 2414.03 for amendments adding to, deleting from, or replacing
 sequence information under 37 CFR 1.835(b)(2) - (4) .
 

 ─ Amino acid sequences required to be included in a
 “Sequence Listing XML” include those comprising D-amino acids, modified amino acids and
 linear portions of branched sequences. 
 

 ─ Nucleotide sequences required to be included in a
 “Sequence Listing XML” include those comprising modified nucleotides, nucleotide analogs
 and linear portions of branched sequences. 
 

 ─Sequences of <10 nucleotides and <4 amino acids are
 prohibited in a “Sequence Listing XML.” 
 

 ─ Uracil is represented by “t” in RNA and DNA, and is
 considered to be a modified nucleotide that requires additional annotation when present in
 a DNA sequence. 
 

 ─ Thymine is represented by “t” in RNA and DNA, and is
 considered to be a modified nucleotide that requires additional annotation when present in
 an RNA sequence. 
 

 ─ Amino acid representations are each one letter. 

 ─ Each sequence disclosed in the “Sequence Listing XML”
 must have its sequence identification number (identifier) associated with “SEQ ID NO:” or
 the like designator next to each occurrence within the disclosure, i.e. SEQ ID NO: X. 
 

 ─ Variations of “SEQ ID NO:” format (e.g. “Seq Id No.”) are
 permitted. Parentheses are NOT required; the sequence identifier, however, must be clearly
 separated from the sequence shown in the specification. 
 

 ─ Sequences in figures can have “SEQ ID NO:” or the like
 with the sequence identifier in the figure itself OR in the Brief Description of the
 Drawings, but it does not have to be in both places. 
 

 ─ Each “Sequence Listing XML” filed in a 111(a) application
 must be accompanied by an incorporation by reference statement that includes the name of
 the file, the date of creation, and the size of the file in bytes. 
 

 ─ A “Sequence Listing XML” filed along with a new
 application need not be accompanied by any statement about new matter. 
 

 ─ An added “Sequence Listing XML” filed after the filing
 date of the application must be accompanied by a statement: • indicating that no new matter
 has been introduced; AND • identifying the support for each new sequence and
 sequence-associated data within the application as filed. 
 

 ─ An amended “Sequence Listing XML,” including one
 submitted to address a defective sequence listing (validated as CRFD), must be accompanied
 by a statement: • indicating that no new matter has been introduced; • identifying the
 locations of additions, deletions or replacements of sequence information relative to the
 replaced listing; AND • identifying the support for the additions, deletions or
 replacements of sequence information within the application as filed. 
 

 ─ The international filing date (PCT filing date) is
 controlling for submission of a sequence listing in compliance with WIPO Standard ST.26 in
 35 U.S.C.
 371 (national stage) applications. 
 

 ─ A sequence listing as an XML file in compliance with WIPO
 Standard ST.26 that is part of the description of an international (PCT) application and
 transmitted by the International Bureau of WIPO to the USPTO upon entry into the national
 phase does not require amendment of the specification of the application to add a statement
 about incorporation by reference, and no statement about new matter is needed. 
 

 ─ A sequence listing as an XML file in compliance with WIPO
 Standard ST.26 that is part of the description of an international (PCT) application and
 transmitted by the International Bureau of WIPO to the USPTO upon entry into the national
 phase does not need to be amended to update bibliographic data, such as the 371 application
 number. 
 

 ─ In cases where no sequence is present in a “Sequence
 Listing XML” for a sequence identification number, i.e. an intentionally skipped sequence,
 “000” is entered as the sequence. 
 

 ─ Sequences that are prohibited from inclusion in a
 “Sequence Listing XML” may be presented within the description, but should not be
 associated with a sequence identification number. 
 

 [top] 

 

 

 
 

 
 

 

 

 

 
 
 
 2401-Introduction 

 2402-The Deposit Rules 

 2403-Deposit of Biological Material 
 2403.01-Material Capable of Self- Replication 

 2403.02-Plant Material 

 
 

 2404-Need or Opportunity to Make a Deposit 
 2404.01-Biological Material That Is Known and Readily Available to the Public 

 2404.02-Biological Material That Can Be Made or Isolated Without Undue Experimentation 

 2404.03-Reference to a Deposit in the Specification 

 
 

 2405-Acceptable Depository 

 2406-Time of Making an Original Deposit 
 2406.01-Description in Application Specification 

 2406.02-Deposit After Filing Date - Corroboration 

 2406.03-Possible Loss of U.S. Filing Date in Other Countries 

 
 

 2407-Replacement or Supplement of Deposit 
 2407.01-In a Pending Application 

 2407.02-After a Patent Has Issued 

 2407.03-Failure to Replace 

 2407.04-Treatment of Replacement 

 2407.05-Exemption From Replacement 

 2407.06-Replacement May Not Be Recognized 

 
 

 2408-Term of Deposit 

 2409-Viability of Deposit 

 2410-Furnishing of Samples 
 2410.01-Conditions of Deposit 

 2410.02-Certification of Statement of Availability of Deposit 

 
 

 2411-Examination Procedures 
 2411.01-Rejections Based on Deposit Issue 

 2411.02-Replies to Rejections Based on Deposit Issue 

 2411.03-Application in Condition for Allowance Except for Deposit 

 2411.04-[Reserved] 

 2411.05-Content of Application with Respect to Deposited Material 

 
 

 2412-The Requirements for Patent Applications Containing Nucleotide Sequence and/or Amino Acid Sequence Disclosures to Include
 a Sequence Listing in XML file format 
 2412.01-Overview of the Sequence Rules 

 2412.02-Definition of “Sequence Listing XML” 
 2412.02(a)-“Enumeration of its residues” 

 
 

 2412.03-Nucleotides and Amino Acids Included and Excluded From a “Sequence Listing XML” 
 2412.03(a)-“Specifically Defined” 

 2412.03(b)-“Amino Acid” 

 2412.03(c)-“Modified Amino Acid” 

 2412.03(d)-“Nucleotide” 

 2412.03(e)-“Modified Nucleotide” 

 
 

 2412.04-Use of Sequence Identifiers to Denote Sequences Disclosed in the Description, Drawings or Claims 

 2412.05-Representation and Symbols for Nucleotide and/or Amino Acid Sequences 
 2412.05(a)-Use of Sequentially Numbered Sequence Identifiers in the “Sequence Listing XML” 

 2412.05(b)-Representation and Symbols of Nucleotide Sequence Data 

 2412.05(c)-Representation and Inclusion of Variants 

 2412.05(d)-Representation and Symbols of Amino Acid Sequence Data 

 2412.05(e)-Presentation of Special Situations 

 
 

 2412.06-The Requirement for Exclusive Conformance; Sequences Presented in Drawing Figures 

 2412.07-Examination of Patent Applications Claiming Large Numbers of Nucleotide Sequences 

 
 

 2413-Content of a “Sequence Listing XML” and Form and Format of the “Sequence Listing XML” File 
 2413.01-Parts of the “Sequence Listing XML” 
 2413.01(a)-The “Sequence Listing XML” is a Single File Encoded Using Unicode UTF-8 

 2413.01(b)-The “Sequence Listing XML” Must Be Valid According To the DTD 

 2413.01(c)-The “Sequence Listing XML” Must Contain an XML Declaration 

 2413.01(d)-The “Sequence Listing XML” Must Contain a DOCTYPE Declaration 

 2413.01(e)-The “Sequence Listing XML” Must Contain a Root Element 

 2413.01(f)-The “Sequence Listing XML” Must Contain a General Information Part 

 2413.01(g)-The “Sequence Listing XML” Must Contain a Sequence Data Part 

 2413.01(h)-Language Dependent Free Text Qualifier Values in the English Language 

 2413.01(i)-Title Element in “Sequence Listing XML” 

 
 

 2413.02-Form and Format of the XML file containing the “Sequence Listing XML” 

 2413.03-How to Submit the “Sequence Listing XML” 

 2413.04-Requirements Regarding Incorporation By Reference of the “Sequence Listing XML” 

 2413.05-Presumptions Regarding Compliance 

 
 

 2414-Notification of a Failure to Comply with Sequence Listing Requirements and Amendments Relating to “Sequence Listing XML” Files
 Under 37 CFR 1.835 
 2414.01-Issuance of a Notice Relating to the Requirements For Patent Applications Containing Nucleotide and/or Amino Acid Sequence
 Disclosures 

 2414.02-Amendment to Add an Initial “Sequence Listing XML” under 37 CFR 1.835(a) 

 2414.03-Amendment Adding to, Deleting from, or Replacing Sequence Information in a “Sequence Listing XML” under 37 CFR 1.835(b) 

 2414.04-Translation of “Sequence Listing XML” is Not an Amended “Sequence Listing XML” under 37 CFR 1.835(b) 

 2414.05-Notifications for Failure to Submit a “Sequence Listing XML” in an International Application under the PCT to be Searched
 by the United States International Searching Authority or Examined by International Preliminary Examination Authority 

 2414.06-Amendment of a “Sequence Listing XML” in a Patent 

 
 

 2415-Applicability date of “Sequence Listing XML” Requirements to Applications Based on Filing Date of Application and Procedures
 for Failure to Submit Correct Format of Sequence Listing 
 2415.01-Determining if a “Sequence Listing XML” Must be Submitted 

 2415.02-Provisional Applications Containing Disclosures of Nucleotides and/or Amino Acids, Compliance with 37 CFR 1.831-1.834 

 2415.03-Improper Submissions of “Sequence Listing” under 1.821(c) When a “Sequence Listing XML” was Required 

 
 

 2416-Form Paragraphs 

 2417-Helpful Hints for Sequence Rules Compliance under WIPO Standard ST.26 

 2418-WIPO Sequence Tool 

 2419-Publishing of Patent Grants and Patent Application Publications with a “Sequence Listing XML” 
 2419.01-Patent Grants and Patent Application Publications Containing a Non-Lengthy “Sequence Listing XML” 

 2419.02-Patent Grants and Patent Application Publications Containing a Lengthy “Sequence Listing XML” 

 2419.03-Patent Grants and Patent Application Publications Containing a “Sequence Listing XML” of 1GB or Larger 

 
 

 2420-The Requirements for Patent Applications Containing Nucleotide Sequence and/or Amino Acid Sequence Disclosures under World
 Intellectual Property Office Standard ST.25 (WIPO ST.25) - the Sequence Rules 

 2421-Overview of the Sequence Rules under WIPO ST.25 
 2421.01-Definition of “Sequence Listing” and Computer Readable Form (CRF) 

 2421.02-Summary of the Requirements of the Sequence Rules 

 2421.03-Notification of a Failure to Comply 

 2421.04-[Reserved] 

 
 

 2422-Nucleotide and/or Amino Acid Sequence Disclosures in Patent Applications Subject to WIPO ST.25 
 2422.01-Nucleotide and/or Amino Acids Disclosures Requiring a “Sequence Listing” 

 2422.02-The Requirement for Exclusive Conformance; Sequences Presented in Drawing Figures 

 2422.03-Sequence Listing Submission 

 2422.03(a)-“Sequence Listing” Submitted as ASCII Plain Text Files 

 2422.04-The Requirement for a Computer Readable Copy of the “Sequence Listing” 

 2422.05-[Reserved] 

 2422.06-Requirement for Statement Regarding Information Contained in the “Sequence Listing” and Separate Computer Readable Form 

 2422.07-Requirements for Compliance and Consequences of Non-Compliance 

 2422.08-Presumptions Regarding Compliance 

 2422.09-[Reserved] 

 
 

 2423-Symbols and Format To Be Used for Nucleotide and/or Amino Acid Sequence Data for WIPO ST.25 
 2423.01-Format and Symbols To Be Used in a “Sequence Listing” 

 2423.02-Depiction of Coding Regions 

 2423.03-Presentation and Numbering of Sequences 

 
 

 2424-Requirements for Content of a “Sequence Listing” Part of the Specification under WIPO ST.25. 
 2424.01-Informational Requirements for the “Sequence Listing” 

 2424.02-“Sequence Listing” Numeric Identifiers 

 2424.03-Additional Miscellaneous Requirements 

 
 

 2425-Form and Format for a Nucleotide and/or Amino Acid Sequence Submission as an ASCII Plain Text File under WIPO ST.25 

 2426-Amendments to Add or Replace a “Sequence Listing” and CRF Copy Thereof Subject to WIPO ST. 25 

 2427-Form Paragraphs for Applications Subject to WIPO ST.25 

 2428-Sample Statements under WIPO ST.25 

 2429-Helpful Hints for Sequence Rules Compliance under WIPO ST.25 

 2430-PatentIn Information 

 2431-Sample “Sequence Listing” under WIPO ST.25 

 2432-[Reserved] 

 2433-Box Sequence; Hand Delivery of a “Sequence Listing” and Computer Readable Forms 

 2434-Examination of Patent Applications Claiming Large Numbers of Nucleotide Sequences 

 2435-Publishing of Patents and Patent Application Publications with a Lengthy “Sequence Listing” 

 

 

 
 

 
 
 

 
 

 

 
 
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 Last Modified: 
 
 03/09/2026 20:49:35