6.1.18.1 Background Nucleotide and/or Amino Acid Sequence Listings

Also in this Chapter:​​​​​​​

• 6.1.18.2 Office Practice

• 6.1.18.3 Summary

Key Legislation:

Articles of the PCT:

• Article 14 Certain Defects in the International Application

• Article 34 Procedure Before the International Preliminary Examining Authority

Administrative Instructions under the PCT:

• s208 Sequence Listings

• s513 Sequence Listings

• s801 Third Party Observation System

• Annex C INSTRUCTIONS RELATING TO THE PRESENTATION OF NUCLEOTIDE AND AMINO ACID SEQUENCE LISTINGS IN INTERNATIONAL PATENT APPLICATIONS UNDER THE PCT

​​​​​​​Regulations under the PCT:

• Rule 5.2 Nucleotide and/or Amino Acid Sequence Disclosure

• Rule 13ter Nucleotide and/or Amino Acid Sequence Listings

• RIO - Processing PCT Tasks - Box I

• RIO - Processing PCT Tasks - Box VII

Related Chapters:

• 6.1.8.2 The Three Person Team (3PT)

• 6.3.8.8 Box VII Certain Defects

• RIO - Processing PCT Tasks - Box I

• RIO - Processing PCT Tasks - Box VII

On this page

• Introduction

  • Whether the listing forms part of the pamphlet

• Examiner workflow: PCT applications filed on or after 1 July 2022

  • Communication with applicant when requirements not met

  • Considering the applicant’s response

• PCT applications filed before 1 July 2022

  • Non-compliance with formalities

• Examiner process flow chart

Note: As of 1 July 2022, WIPO implemented the ST.26 Standard. All applications with a filing date of 1 July onwards will need to be processed based on the procedures set out in 6.1.18.2 Office Practice and 6.1.18.3 Summary.

Introduction

Nucleotide and/or amino acid sequence listings are representations of the sequence in a standardised format set down in Annex C of the Administrative Instructions under the Patent Cooperation Treaty. This listing(s) may be supplied with an international application in addition to the sequence disclosed in the specification.

The following definitions apply:

• Nucleotide sequence: an unbranched sequence of ten or more contiguous nucleotides

• Amino acid sequence: an unbranched sequence of four or more contiguous amino acids

Branched sequences of either nucleotide or amino acids are specifically excluded (Annex C).

Note: A sequence listing is a separate part of the description that is presented in a specific format (Annex C). Nucleotide or amino acid sequences that appear in the figures or drawings, or in the text of the description, do not constitute a sequence listing.

Whether the listing forms part of the pamphlet

The listing may be either:

• filed as part of the specification

• furnished separately at a later date

In either of the following circumstances, the sequence listing forms part of the description (Rule 5.2) and hence forms part of the pamphlet:

• Where the sequence listing was originally filed as part of the description

• Where it was filed in response to an Article 14 objection (certain defects in the specification) by the Receiving Office

However, if the sequence listing is only filed in response to a Rule 13ter request by the International Searching Authority (ISA) then the sequence listing does not form part of the description (unless the subject of an Article 34 amendment) and will not be part of the pamphlet (Rule 13ter(f)).

Examiner workflow: PCT applications filed on or after 1 July 2022

Note: a flow chart of the examiner workflow is provided at the end of this page.

Where the international application contains a disclosure of a nucleotide and/or amino acid sequence, it must be accompanied by sequence listing that is compliant with WIPO ST.26 Standard. The standard requires the listing to be provided in XML format.

After initial processing of the application by PCT unit, the application will be forwarded along with the attached sequence listing to the relevant examination section. The relevant examination section will then determine if the provided XML sequence listing complies with WIPO ST.26. The examiner inputs the sequence listing into the WIPO sequence validation tool which then validates whether the sequence is in the required format. The examiner then places a copy of the validation report produced by the WIPO sequence tool on file for dispatch to the applicant by the PCT unit. 

Communication with applicant when requirements not met

Where the provided XML sequence listing does not comply with WIPO ST.26 standard, the applicant is to be advised via a comment in Box VII of PCT/ISA/237 (see 6.3.8.8 Box VII Certain Defects and RIO – Box VII). Examiners are to then to establish the opinion to the extent that a meaningful search could be carried out without a WIPO ST.26 compliant listing.

Where the application does not contain a separate sequence listing in XML format, examiners should request a sequence listing under Rule 13ter.1(a). The sequence listing provided must be in an electronic form and accompanied by a statement to the effect that does not include matter which goes beyond the disclosure in the international application as filed. 

Considering the applicant’s response

Where a statement regarding added subject matter is not available to the competent authority, any such correction, rectification or amendment need only be taken into account by that authority for the purposes of the international search or preliminary examination to the extent that a meaningful search or preliminary examination can be carried out without such a sequence listing in electronic form.

If the applicant does not comply with an invitation, the ISA will only search the international application to the extent that a meaningful search can be carried out without the sequence listing (Rule 13ter.1(c)).

Any limitations placed upon the scope of the search, as a result of non-compliance with this request, should be discussed by the 3-person team (see 6.1.8.2 The Three Person Team (3PT)).

Note: A sequence listing provided in response to a Rule 13ter request does not form part of the international application

PCT applications filed before 1 July 2022

A full flow chart of the examiner workflow is provided at the end of this page.

Where the international application contains a disclosure of a nucleotide and/or amino acid sequence, the sequence listing may be in paper form, or electronic form on a (ISO9660) CD-ROM, CD-R or DVD. According to Section 208 of the Administrative Instructions, the standard prescribed for a sequence listing is that specified in Annex C (see Rule 5.2 and Administrative Instructions 208 & 801).

As of 1 July 2009, the filing of 'mixed mode' PCT applications (international applications where the sequence listing is filed in electronic form and the remainder of the international application is filed in paper form) is not permitted. Therefore, international applications must be filed in either paper or electronic form in order to be accepted by the Receiving Office.

When an international application containing a sequence listing is lodged with the Receiving Office, the PCT unit will check that the necessary formalities requirements have been met before the application is forwarded to the relevant examination section.

Note: An application where the sequence listing is provided in paper form may also contain a copy of the sequence listing in electronic form in order to comply with Rule 13ter (see Administrative Instruction 208 and Administrative Instruction at Annex C).

Non-compliance with formalities

If the sequence listing provided at filing is not in electronic form, or if one is provided which does not comply with Annex C, the ISA may issue an invitation to the applicant to either (under Rule 13ter.1(a)):

• furnish a sequence listing in electronic form

• furnish a listing which complies with Annex C

The sequence listing provided must be in electronic form encoded as a text file on CD or DVD media. The prescribed time for responding to such an invitation is usually one month. See also: RIO guidance for PCT/ISA/225, PCT Rule 13ter.1(a), and Ad. Inst. 513(a).

If the applicant does not comply with an invitation, the ISA will only search the international application to the extent that a meaningful search can be carried out without the sequence listing (see Rule 13ter.1(c)).

Any limitations placed upon the scope of the search as a result of non-compliance with this request should be discussed by the 3-person team (see 6.1.8.2 The Three Person Team (3PT)).

Examiner process flow chart