PA 07/2009: The options available for the filing of international applications containing sequence listings

WARNING: Although the information which follows was correct at the time of original publication in the PCT Newsletter, some information may no longer be applicable; for example, amendments may have been made to the PCT Regulations and Administrative Instructions, as well as to PCT Forms, since the PCT Newsletter concerned was published; changes to certain fees and references to certain publications may no longer be valid. Wherever there is a reference to a PCT Rule, please check carefully whether the Rule in force at the date of publication of the advice has since been amended.

Q:  I have heard that a number of changes took place on 1 July 2009 concerning the filing of sequence listings, for example, that there is no longer a fee benefit for sequence listings over 400 pages.  As I plan on filing an international application containing a sequence listing of about 500 pages, please could you explain the options available to me for filing the sequence listing part – will I now have to pay a fee per sheet for that part?

A:  It is recalled that where international applications disclose nucleotide and/or amino acid sequences, a sequence listing must be presented as a separate part of the description (“sequence listing part of the description”) in accordance with PCT Rule 5.2(a) and the Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in PCT applications which is contained in Annex C of the Administrative Instructions under the PCT.

Former Part 8 of the Administrative Instructions (Sections 801 to 806), which permitted the filing of the sequence listing part of the international application to be filed in electronic form on a physical medium (for example, a CD), together with the remainder of the application on paper (sometimes referred to as “mixed-mode” filings), was introduced in 2001 as a temporary solution to problems arising from the filing of very large sequence listings on paper, which were difficult to handle for applicants and Offices and very expensive for applicants.  Now that applicants may, and do to an increasing extent, file international applications in electronic form, such temporary provisions have become less relevant, and Part 8 of the Administrative Instructions has been deleted with effect from 1 July 2009. 

Although the benefit of paying a maximum of 400 times the fee per sheet of sequence listing, regardless of the length of the sequence listing, is no longer available to applicants subsequent to the deletion of Part 8 of the Administrative Instructions, the newly modified Administrative Instructions governing the filing of sequence listings will, in general, be beneficial to applicants, International Authorities and designated Offices, as will be explained below. 

For international applications filed on or after 1 July 2009, according to modified Section 707(a‑bis) of the Administrative Instructions, where a sequence listing is contained in an international application filed in electronic form (presuming that the receiving Office concerned is prepared to accept international applications in the electronic forms concerned), the calculation of the international filing fee should not take into account any sheet of the sequence listing if that listing is presented as a separate part of the description in accordance with PCT Rule 5.2(a) and is in the electronic document format specified in the sequence listing standard in the Administrative Instructions, Annex C, paragraph 40 (hereinafter: “text format”).  That is, you do not pay any page fees at all for the sequence listing if the international application is filed in electronic form and the sequence listing is provided as a text file in the appropriate format, for example as output from the dedicated PatentIn software (available free of charge from the European Patent Office website at:, or from the United States Patent and Trademark Office (USPTO) website at:  You will also benefit from the fee reductions (of between 100 and 300 Swiss francs, depending on the type of filing involved) which apply generally to electronic filings.

Moreover, by providing the sequence listing in text format, the sequence listing should also be usable, under PCT Rule 13ter, for the purposes of international search (and examination) and there will be no need to file a second copy for that purpose.

The other, albeit more costly options, for filing sequence listings are:

(1)     filing the international application in electronic form, including the sequence listing in electronic form, but in an image format, rather than in a text format (for example, having converted the text format to PDF format); or

(2)     filing the international application on paper, in which case the sequence listing must also be included in paper form (as would be the case, for instance, where the application is filed using the PCT‑EASY functionality of the PCT‑SAFE software).  In the case of paper filings, only sequence listings filed for the purposes of international search under PCT Rule 13ter may be filed in electronic form on a physical medium.

In both of the above cases, you would have to pay full page fees for the entire application, including for each page of the sequence listing in image format.  Therefore, in terms of fees payable, this option would seem to be feasible where there are only a small number of pages of sequence listings in the application.  Furthermore, you may in any case be invited to furnish a sequence listing in text format for the International Searching Authority (ISA) (and, where applicable, the International Preliminary Examining Authority (IPEA)) for search (or examination) purposes only, and if this is furnished later in response to an invitation by the ISA or IPEA, a late furnishing fee may be payable to the Authority concerned (PCT Rule 13ter.1(c)). 

Note that if your international application contains tables related to sequence listings, these tables must be included as an integral part of the description in the same format as the remainder of the application, that is, where the international application is filed on paper, any tables must also be included on paper.  The pages containing such tables will count as regular pages of description, irrespective of the format in which they are submitted (whether on paper or in electronic form) (noting that such pages are not machine-readable in the way that sequence listings in text format are).

Applicants filing international applications with the USPTO as receiving Office (RO/US) should note that the e-filing system of the USPTO, EFS‑Web, permits two methods of filing the sequence listing with the application:

(1)     the sequence listing may be uploaded directly along with the body of the international application – in this case, the file should preferably be in text format (without page fees) but may be in PDF format (with full page fees);  or

(2)     in the case of a sequence listing larger than 100 MB, it may be deposited separately on a physical medium (CD) at the USPTO on the same day as the international filing date – in this case, the file may only be in text format.

Applicants filing an international application containing tables related to sequence listings with RO/US via EFS‑Web should note that these tables must be an integral part of the description in PDF format only (with full page fees payable).

The revised Administrative Instructions relating to the filing of sequence listings in text format therefore encourage applicants to furnish the sequence listings in a format which is not cumbersome, is searchable and can therefore be used for search and examination purposes as well as for disclosure, can be used by the designated Offices in the national phase, and which enables applicants to save money by not having to pay any page fees.

Applicants are reminded to use the July 2009 version of the request form (PCT/RO/101), which has been revised to take into account the above-mentioned changes, when filing international applications on or after 1 July 2009.  It is recalled that there are two alternative last sheets of the request form:  the one which is headed “CHECK LIST for PAPER filings” should be used if the applicant intends to file the international application on paper;  the one which is headed “CHECK LIST for EFS‑Web filings” should only be used if the applicant intends to file the request form online with the USPTO as receiving Office via EFS‑Web.  A new version of the PCT‑SAFE software, which takes into account the new method of page fee calculation, is available at:

For applicants who are not able to upgrade their existing PCT‑SAFE installation immediately, where a text file has been uploaded, it is possible to manually change the “number of pages” for the sequence listing to zero, which will then give the correct fee calculation.  Note, however, that if the sequence listing is filed in PDF format and is more than 400 pages long, the fee calculation will be incorrect if using an earlier version of the software because it only counts to a maximum of 400 pages for the sequence listing, and it is not possible to manually modify the page count in this case.

For further information on the changes regarding the filing of sequence listings and tables related to sequence listings, see the PowerPoint presentation “Amendments to the Regulations and other practice changes – July 1, 2009” at:

The text of the modifications of the Administrative Instructions (as in force from 1 July 2009) concerning sequence listings was published in the Official Notices (PCT Gazette) on 14 May 2009 at:

and the consolidated texts of the Administrative Instructions and Annex F (Standard for Filing and Processing in Electronic Form) are available at:

References: r_5_pct;

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