Description of the genome query for

Selecting ORFs by functional category

The user selects a genome, or the results from his or her last query, and selects a functional category or a group of related functional categories. The query then returns each of the ORFs satisfying the request.

Functional category classification is extrapolated (using a BLASTP cutoff expectation value of 1.0e-5) from the limited data set available from ftp://ftp.ncbi.nih.gov/pub/COG/COGs.txt. These are the "Clusters of Orthologous Groups", which include functional category information.

We classify the remaining ORFs by going through their lists of BLASTP hits and assigning a functional category wherever the hit is to one of NCBI's reference COG ORFs. Assignment to multiple functional categories is fully permissible. One danger in this approach is that proteins with similar domains may be included in the same functional category, even if some of the proteins do not actually serve that function. We would appreciate any suggestions for feasibly tightening the memberships.

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