How To Find Go Numbers Given A Protein Coding Sequence?

Question

[burkhart.joshua]

I have a large collection of protein coding sequences and I'd like to find GO numbers for them in order to categorize them by function. I can automate the NCBI BLAST process, yielding accession numbers (like XM_329174.1, NM_234985.3, etc.), but don't know how to convert those to GO numbers. Is there a database that maps NCBI accession numbers to GO numbers? Also, is there a source that describes the GO hierarchy in a machine-readable form?

[Rm]

Similar to How do I do simple GO term lookup given a gene (or mRNA) identifier?

[Neilfws]

Please search this site for "biomart".

Answer 1

[Björn]

Hi Joshua,

if you start with a sequence you can also try Blast2GO. It is also available as standalone version and has a Galaxy Integration.

Cheers,

Bjoern

Answer 2

[David Westergaard]

Another alternative may be to use Interpro. Iinterpro has started an effort to annotate all HMMs with GO terms, so this might be a valuable addition to your data.

You can use the Interproscan executable for automated command line usage. Runtime is only slighty above that of BLAST.