Is my sequence patented?

It is not always a straightforward task to determine if a sequence of interest is already patented, or is the subject of a pending patent application.   Sequences in claims are referred to by a number designator – e.g., SEQ ID NO: 1.  The sequences themselves are in a separate section called the Sequence Listing.  Unfortunately, in the Sequence Listing, there is usually little annotation of the sequences. Annotation, such as it is, must be teased out of the patent text.

To compare sequences in the Sequence Listing and claims to a selected sequence, there are options.  Free search options include BLAST and CAMBIA’s patent sequence search tool, and pay options include a number of proprietary or subscription based services, such as Thompson-Derwent and Genome Quest.

BLAST

BLAST is a program that finds regions of similarity in biological sequences. It can be used to search for similar nucleotide or amino acid sequences, and also allows searches of a translated nucleotide database using both nucleotide and amino acid queries. To search for patent sequences in BLAST, the patent database must be selected. An oft-used patent database is provided by GenBank, and it contains sequences from granted U.S. patents as well as sequences in published PCT applications and Japanese patents. This search collection currently lacks sequences in U.S. applications, however. Searching with BLAST will identify many patents that contain sequences that are similar to a sequence of interest, but does not differentiate between sequences that are in the Sequence Listing from sequences referenced in claims.

CAMBIA’s Patent Sequence Search Tool

CAMBIA offers a free patent sequence search tool that uses the BLAST search interface. The search collection includes sequences from granted U.S. patents as well as U.S. patent applications, all of the sequences in the GenBank collection, as well as many more sequences that are provided by the USPTO in a different format, e.g., sequences from bulk sequence applications.  An important feature of our search tool is that it allows users to search for patent sequences that are claimed in patents and patent applications rather than sequences that are simply disclosed in the specification.

Claim Language is Key

Claim language is complex and quite variable, and does not lend itself well to automated analysis via software solutions. If a sequence of interest is recited in a patent claim, it is the claim language that ultimately determines if the sequence is patented or not.

Below is an example where a sequence mentioned in the claims is actually claimed as a composition of matter:

An isolated nucleic acid segment comprising the sequence of SEQ ID NO:2.

Alternatively, here is an example of a claim that recites a sequence, but where that sequence is not claimed:

A vector construct comprising the sequence of SEQ ID NO:7 operatively linked to a nitrogen-responsive promoter.

The claim states that the sequence of SEQ ID NO:7 must be “operatively linked to a nitrogen-responsive promoter”. Therefore, the claimed nucleotide encompasses both SEQ ID NO:7 and the promoter, and if your sequence was linked to a different type of promoter, then the use of your sequence would not infringe upon this patent.