When working with new or engineered gene, I typically start with the sequence search to avoid missing something due to differences in nomenclature. My first stop is the NCBI's BLAST (Basic Local Alignment Search Tool) site which allows me to find regions of homology between my DNA and/or protein sequence and entries in the NCBI sequence database. A typical output includes a list of genes with homologous sequences, the statistical significance of the matches and information on functional and evolutionary relationships.
I supplement this information by searching US patents and patent applications for my new gene sequence. This process is made easy using a search utility developed by Cambia's Patent Lens Sequence Project. This search site uses NCBI's BLAST software to search sequences that are listed in the specifications and claims of US patents and published patent applications. Below is a sample output from a search of Mus musculus erythropoietin (EPO) mRNA sequence in the Cambia database. The numerical score in the search result is a hypertext link to information that provides more detailed alignment and homology data.
Sequences producing significant alignments: Score gb|AR308789.1|AR308789 Sequence 3 from Patent US6555343 250 gb|GV939069.1|GV939069 Sequence 11 from Patent US74... 248 gb|AR926143.1|AR926143 Sequence 12 from Patent US70... 244 gb|GZ136886.1|GZ136886 Sequence 21 from Patent US81... 228 gb|GZ136885.1|GZ136885 Sequence 20 from Patent US81... 228 USRE40911_2 Sequence 2 from Patent USRE40911 208 gb|AR477490.1|AR477490 Sequence 2 from Patent US6696411 208 gb|GC662854.1|GC662854 Sequence 5 from Patent US744... 202
The sequence data in the Cambia system is a little out of date but it often gives me a starting point for more detailed patent searching.