Is my sequence patented?

It is not always a straightforward task to determine if a sequence of interest in is already patented, or is the subject of a pending patent application. There are a couple of free search options; BLAST and CAMBIA's patent sequence search tool, and a number of proprietary or subscription based ones, 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. The patent database is provided by GenBank, and contains sequences from granted US patents as well as sequences in published PCT applications and Japanese patents. However, this search collection currently lacks US applications. Searching with BLAST will identify many patent applications that contain sequences that are similar to a sequence of interest, but does not differentiate between sequences that are disclosed in the specification from sequences referenced in claims.

CAMBIA's Patent Sequence Search Tool

CAMBIA now offers a free patent search tool with an interface similar to the BLAST search interface. The search collection includes both granted US patents as well as US 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. The CAMBIA sequence search collection includes all of the sequences in the GenBank collection, as well as many more sequences that are provided by the USPTO in a different format, such as sequences from bulk sequence applications.

Claim Language is Key

Even if a sequence of interest is referenced in a patent claim, it is the claim language that ultimately determines if the sequence is patented or not. For example, a claim that reads:

Nucleotide sequences that encode the amino acid sequence of SEQ ID NO:36

It might initially appear that SEQ ID NO:36, an amino acid sequence is encompassed by the claim. Rather, SEQ ID NO:36 is not included in the claim, but any nucleotide sequence that encodes it is.

• NCBI resources (and European and Japanese repositories): 

          - patnt, pataa:  fill in the missing sequences

          - completely sequenced genomes and much other sequence

• Include amino acid sequences and translated or reverse-translated searches where these are claimed

• Include not only sequences explicitly claimed but also those included by similarity, complementarity claims

• Separate analysis for sequences in pending claims (patnt and pataa include the sequences only from granted patents)

• Informatics around patent status and assignees

• Comments  (USPTO experiment starting next year;  EPO/WIPO?)

Help is welcome in this collaborative project