Umm, What Exactly Do I Need to File a Sequence Listing via EFS?

In recent years, patent offices have embraced various technological advancements.  For example, five years ago US biotech patent applications/responses were largely filed via paper and disk (later a “disc”) with few opting for electronic submission.  That has undoubtedly been turn upside-down with the vast majority now filed via the Electronic Filing System (EFS).  Though these innovations theoretically allow for more efficient filing processes and faster response times, many aspects have not been updated on the same timeline.

We receive questions all the time regarding the language and specific requests outlined in generic Notices from the USPTO with regards to filing via EFS.   With that in mind, let me clarify a few of the most common inconsistencies seen in a Notice to Comply, Notice to File Missing Parts, and Notice to File Corrected Application Papers, etc:

1.     “This application does not contain, as a separate part of the disclosure on paper copy, a “Sequence Listing” as required by 37 CFR 1.821(c)…”

CLARIFICATION: Sequence Listings are NOT required to be in paper form as they can be uploaded directly onto PAIR via EFS.  Further, when a Sequence Listing is filed electronically, page fees are not charged, however, when/if supplemented with a PDF copy of the Sequence Listing, page fees are often applied.

2.     “Applicant must provide an initial paper or compact disc copy of the “Sequence Listing”…”

CLARIFICATION:  This is outdated language that does not necessarily apply to EFS submission or paper and disc filing.  When filing via paper and disc, the applicant must submit a paper copy and a compact disc copy, not or a compact disc copy.  When filing via EFS, the applicant need only file the text copy of the sequence listing.

3.     “…as well as an amendment specifically directing its entry into the application…”

CLARIFICATION: “An amendment specifically directing its [Sequence Listing] entry into the application” is only required when filing via EFS.  It is not required if filed via paper and disc.

4.     “…and a statement that the content of the sequence listing information recorded in computer readable form is identical to the written (on paper or compact disc) sequence listing…”

CLARIFICATION: Again, please see Points 1 and 2 above – a paper copy is not required.  Furthermore, the passage continues on to reference 37 CFR 1.821(e) wherein the same terminology is present, which implies that the CFR itself has yet to embrace the USPTO’s own advancements in technology.

5.     Possibly the most obvious support of not keeping up with the times is the omission of the fact that you can file via EFS and what exactly is required to do so.

6.     This last issue does not directly come from any specific Notice, however, it is directly related.  A statement is required to be filed along with a Sequence Listing.  That’s a fact.  The statement attests that the sequences in the Sequence Listing are identical to those in the application and does not contain any new matter (if applicable).  So who should sign it?  The attorney or the preparer?  The answer is personal preference, as the CFR does not require that the signer be of record.

Bottom line, and in the simplest terms, to satisfy the Sequence Listing requirements when filing via EFS, all that is necessary is a text copy (.txt) of the Sequence Listing, a statement attesting that the sequences in the Sequence Listing are identical to those in the application and does not contain any new matter (if applicable), and a paragraph incorporating the same.

-The Harbor Consulting Team

For more information regarding Harbor Consulting, please visit www.seqidno.com.

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“Neither Alpha or Numeric.” What a pain in the ASCII!

Preparing Sequence Listings on a daily basis helps keep those of us here at HCIP “in the know” with regards to what the patent office finds acceptable (and not acceptable) in Sequence Listing disclosures.  That being said, the USPTO does its best to provide updated free-of-charge software to assist in the preparation of Sequence Listings.  However, does this software prepare a listing that will be fully compliant with Sequence Listing requirements?

The answer to this question is “rarely.”

For the most part, the PatentIn software is sufficient.  That said, however, a big limitation of this software is the inability to distinguish a non-ASCII character from an ASCII character which therefore allows non-ASCII characters to be incorporated into your listing.  As we all know, Sequence Listings must be submitted in ASCII text, meaning the incorporation of non-ASCII characters WILL garner a rejection.

So how do these non-ASCII characters get into your listing?  The most common way is by “copying and pasting” data directly from your patent application into the sequence files or the PatentIn program.  When this happens, the character will not be rejected or produce an error notification until you try to run your listing through the Checker program.

Checker will inform you that the “Input File is neither Numeric or Alpha.”  You WILL NOT receive any indication as to what the character in question is, or even where in your document this character may be.  IF your listing is relatively short, say a handful of sequences, you can scroll through the document and hopefully find it by eye easily enough.  However, and this is a BIG HOWEVER, if your listing is lengthy, as many listings are, you may find yourself scrolling through hundreds or thousands of sequences, or worse yet, thousands of pages.

As you can imagine, this can be a very tedious and daunting task.  So how do you avoid the incorporation of these characters into your listing?  Be EXTREMELY careful!  Be sure to thoroughly review the data incorporated not only into the sequence files, but the cursory data as well, and when possible, hand-key anything that is a symbol or looks “suspicious.”

-The Harbor Consulting Team

For more information regarding Harbor Consulting, please visit www.seqidno.com.

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