By Christopher P. Singer --
Since the launch of EFS-Web in the fall of 2006, applicants have had the option of e-filing sequence listings as text (.txt) files only, rather than filing sequence listings in both paper and computer readable copies. Several biotech prosecutors in our office have had recent discussion and debate about what files and statements can or must be filed with an EFS-Web filed sequence listing in order to be compliant with the requirements under the Legal Framework and in order for it to be considered as part of the original application.
As we discussed in November 2006 (see "Hassle-Free Filing of Sequence Listings on EFS-Web Version 1.1"), the early version of EFS-Web was limited because it allowed submission of files in .pdf format only and was not able to handle sequence listing filings because they needed to be submitted as text files (.txt). Since the upgrade to EFS-Web 1.1 in October of 2006, practitioners have been able to electronically submit text files such as sequence listings, computer program listings, and mega tables. This eliminated the need to submit these types of files on supplemental electronic media (e.g., CD-R, 3.5" disk, etc.) and avoid fees for excess application size (currently $270 for large entities or $135 for small entities per 50 pages after the first 100).
Section XIII of the EFS-Web Legal Framework clearly authorizes the filing of a sequence listing as a text file (37 C.F.R. § 1.821(c)), provided the file is ASCII compliant. When submitting a sequence listing in this way, 37 C.F.R. § 1.52(e)(5) requires that the specification be amended to contain an incorporation-by-reference of the material in the text file in a separate paragraph which identifies the name of the text file, the date of its creation, and the size of the text file in bytes. This paragraph should be inserted immediately before the Background of the Invention (37 C.F.R. § 1.77(b)(5)). Pursuant to 37 C.F.R. § 1.821, a patent application which discloses nucleotide and/or amino acid sequences must contain both "a paper copy" of the sequence listing (37 C.F.R. § 1.821(c)) and a computer-readable form (CRF) of the sequence listing (37 C.F.R. § 1.821(e)). As long as the sequence listing text file submitted via EFS-Web is a compliant ASCII text file, it will serve as both the paper copy required by § 1.821(c) and the CRF required by § 1.821(e). Because the single file serves this dual role, the statement indicating that the paper copy and CRF copy of the sequence listing are identical is no longer necessary (37 C.F.R. § 1.821(f)). There is also no need to submit any additional copies of the sequence listing pursuant to § 1.821(e). That is, if the sequence listing text file submitted by EFS-Web is ASCII compliant, the filer should not separately request the use of a compliant computer readable sequence listing that is on file for another application. If such a request is filed, the Office will not carry out the request but will use the sequence listing submitted with the application as originally filed via EFS.
When filing a sequence listing in response to a Notice to Comply or Notice of Missing Parts, you must include a statement indicating that the sequence listing does not include any new matter that goes beyond the disclosure of the application as filed. As with the filing of a sequence listing with an original application, the statement under § 1.821(f) is not necessary, and requests under § 1.821(e) will not be carried out.
Sequence listing text files submitted by EFS-Web have a size limit of 100 megabytes. Because of this size limit, filers with sequence listing files larger than 100 megabytes are encouraged to submit the text file on compact disc via Express Mail (37 C.F.R. § 1.10) on the date of the corresponding EFS-Web filing, if the filer wishes the electronic copy to be considered part of the application as filed. Alternatively, a filer may submit the application in paper and include the electronic copy of the sequence listing text file on compact disc in accordance with 37 C.F.R. § 1.52(e). According to the Legal Framework:
Electronic filing of sequence listing text files in international applications with the U.S. Receiving Office of the PCT is authorized under sections XVII and XVIII of the EFS-Web Legal Framework. Under PCT Rule 5.2(a), the sequence listing is filed as a separate part of the description and should be submitted as a single ASCII text file. The text file will serve both as the written portion of the sequence listing under PCT Rule 5.2 and the electronic form under PCT Rule 13ter.1(a). Furthermore, the required statement in paragraph 40 of Annex C that "the information recorded in the electronic form is identical to the sequence listing in the application" is not required. Similar to U.S. filings, follow-on submissions will form part of the international application if they are filed on the same date on which the international application was filed. EFS-Web can be used to submit a sequence listing in text format after the international filing date in response to a requirement under PCT Rule 13ter, however it will not form part of the international application as set forth in PCT Rule 13ter.1(e).
A noteworthy difference between U.S. and PCT practice concerning the filing of sequence listings in electronic format relates to fees. As noted above, the USPTO does not charge excess page fees for compliant sequence listings submitted by EFS-Web only. However, the PCT does charge a fee for electronically submitting sequence listings only as text files (or on any electronic media). The fee is equivalent to the fee for 400 excess pages (currently $5,600), so filing sequence listings in the PCT as electronic text files only makes economic sense if the sequence listing is over 400 pages in length. For sequence listings that are less than 400 pages, a better alternative is to submit the sequence listing as a .pdf as part of the application (so as to pay only for the pages submitted), while also including the text file of the sequence listing. In this situation, the filer should also submit the statement required by Annex C.