MPEP § 2418 — MPEP § 2418
Current through: 2022-07-01

2418-WIPO Sequence Tool 
 
 

 
 
 
 
 
 
 
 

 

 
 
 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
 
 
 
 

 
 
 
 
 
 
 
 
 
 
 

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 Chapter 2400 

 Section 2418 
 

 
 
 
 
 
 2418 WIPO Sequence Tool [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) .] 

 To comply with rules based on WIPO Standard ST.26 (i.e.,
 37 CFR
 1.831 - 1.835 ), patent applicants can generate
 a compliant “Sequence Listing XML” using WIPO Sequence, a desktop application developed by
 WIPO and adopted by WIPO member states, including the US. WIPO Sequence has two functions:
 An authoring function and a validation function. Patent applicants are able to author and
 validate their “Sequence Listing XML” using WIPO Sequence to comply with the requirements
 of WIPO Standard ST.26. A “Sequence Listing XML” that passes validation by WIPO Sequence
 will be accepted by all the IPOs of the WIPO member states, although translation may be
 needed. Thus, the burden of generating a WIPO Standard ST.26 compliant sequence listing in
 XML file format that is acceptable across all WIPO member states will be significantly
 decreased for patent applicants under WIPO Standard ST.26. This tool is downloadable, free
 of charge, from the WIPO website. The current version of WIPO Sequence is accessible at
 www.wipo.int/standards/en/sequence/index.html . 
 

 The first step to generate a new sequence listing using
 WIPO Sequence is to create a project. The user saves (authors) patent application data and
 biological sequence data in the project, validates the project to ensure all required
 sequence-associated information is present, and generates a “Sequence Listing XML” in
 compliance with 37 CFR 1.831 - 1.834 (complying with WIPO Standard
 ST.26 in XML format). Information can be entered into a project manually, or data can be
 imported from a source file in one of a number of file types. WIPO Sequence can import data
 from other WIPO Standard ST.26 projects, WIPO Standard ST.26 XML sequence listings, WIPO
 Standard ST.25 sequence listing text files, raw data files, multi-sequence format files,
 and FASTA format files. The entry of sequence-associated data, such as feature keys,
 qualifiers, and organism names, are facilitated by their selection from drop-down lists,
 simplifying the creation of a sequence listing. Applicant and inventor names, as well as
 custom organism names, can be stored in WIPO Sequence for easy access from other projects.
 To facilitate the review of data entered into a project, WIPO Sequence can generate a
 “human-readable” version (a text version of the sequence data) of the “Sequence Listing
 XML.” This human readable version must not be submitted in a patent application.
 

 WIPO Sequence includes an integrated validation function
 that will alert users to most errors in a project (i.e., “Sequence Listing XML” data). The
 validation function generates a report that clearly lists every detected error, the
 location of the error, and the detected value of the error, along with a link to the
 sequence in question, thereby ensuring users can correct errors before generating a final
 “Sequence Listing XML.” While the validation function will alert a user to most errors in a
 project or “Sequence Listing XML,” there are a small number of errors that can be detected
 only by human review (for example, an inappropriate organism name). In those cases, the
 integrated validation function will list a “warning” in the validation report, reminding
 users of the applicable/relevant rule and urging them to check their input values before
 generating a final “Sequence Listing XML.” The WIPO Sequence validation function can also
 be used to validate a “Sequence Listing XML” that was previously generated. As for
 validation of a project, the validation of a “Sequence Listing XML” generates a report that
 clearly lists every detected error, the location of the error, and the detected value of
 the error in the “Sequence Listing XML.” It is highly recommended that a “Sequence Listing
 XML” produced by WIPO Sequence be validated following its generation. 
 

 To ensure that IPOs can validate applicant-submitted
 sequence listings generated with WIPO Sequence, WIPO developed a Standard ST.26 sequence
 listing validation tool, WIPO Sequence Validator. WIPO Sequence Validator is for use by
 IPOs to verify that filed sequence listings comply with WIPO Standard ST.26 . WIPO Sequence
 Validator is synchronized with the validation function in the WIPO Sequence tool such that
 WIPO Sequence Validator applies the same validation rules as WIPO Sequence. The USPTO has
 integrated WIPO Sequence Validator into its internal IT systems (i.e., CRFValidator).
 Therefore, filers will have a greater level of confidence that a “Sequence Listing XML”
 validated by WIPO Sequence will comply with the USPTO rules for a “Sequence Listing XML”
 ( 37 CFR
 1.831 through 1.835 ) and be accepted.
 

 A “Sequence Listing” in WIPO Standard ST.25 format cannot
 automatically be converted into WIPO Standard ST.26 format primarily because certain data
 elements required for a “Sequence Listing XML” compliant with WIPO Standard ST.26 are not
 present in WIPO Standard ST.25 sequence listing. Therefore, conversion of a “Sequence
 Listing” in WIPO Standard ST.25 format to WIPO Standard ST.26 format necessarily requires
 additional input from the applicant. WIPO Sequence, supplemented by significant guidance in
 Annex VI and Annex VII of WIPO Standard ST.26, will help applicants to accomplish this task
 without added or deleted subject matter. Users can import a WIPO Standard ST.25 “Sequence
 Listing” into a project, and WIPO Sequence automatically performs many of the necessary
 conversions. An Import Report is generated that alerts the user to all data conversions and
 lists all sequence entries that require additional input. In response to concerns raised
 regarding the USPTO’s requests for comments in 2012 and 2016, the USPTO, in conjunction
 with WIPO, developed Annex VII to provide detailed guidance to help applicants avoid added
 or deleted subject matter when converting a “Sequence Listing” in WIPO Standard ST.25
 format into a WIPO Standard ST.26 “Sequence Listing XML” format. 
 

 A sample sequence listing (XML file) specimen can be found
 in WIPO Standard ST.26, Annex III and at www.wipo.int/standards/en/xml_material/st26/
 st26-annex-iii-sequence-listing-specimen.xml .
 

 [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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 03/09/2026 20:49:35