[BioPython] GO term annotation from fasta?

[Davis, Sean (NIH/NCI) [E]]

-----Original Message-----
From: Alan Wardroper [mailto:biopython at wardroper.org]
Sent: Fri 12/22/2006 10:58 PM
To: biopython at lists.open-bio.org
Subject: Re: [BioPython] GO term annotation from fasta?
 
>Alan Wardroper wrote:
>> I have a large db of est clones and associated assemblies I'd like to
>> (roughly) annotate using GO terms ... with biopython.

>In what species are you working?

Salmonids-- at this point mostly Salmo salar and Oncorhynchus mykiss,
but also others down the line.

-------------------------

Your original solution sounds reasonable, but you might want to thing about some sort of translated blast, as I don't suppose your organism(s) are very similar to any of the well-annotated genomes.  Also, blasting against genbank won't get you much, as most the genbank accessions are not annotated in GO.  You might consider blasting against the sequences in GO (which are proteins, I believe, and are available in the GO database), so you could map directly from your sequences to best blast hit to GO.

Sean

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