[BiO BB] Is it possible to Blast against genBank files
idoerg at burnham.org
Thu Dec 18 16:00:25 EST 2003
Biopython has something that can do that. Maybe Bioperl too. Let me know
if you want the Python code.
jordan swanson wrote:
>>You mean that the BLAST results only have the Fasta
>>file annotation in
>>them. Well, AFAIK, the only input to formatdb is
>>Fasta or ASN.1. The
>>output, anyhow, would be a one-liner.
>>How about giving her the output in HTML (-T option)?
>>builds a link from each hit to the NCBI page. So
>>using a browser, your
>>coworker can skim the one-line annotation, and then
>>click & delve into
>>the more interesting ones.
> We did try that, however with the large number of
> sequences she needed to look up, she was black-listed
> from their machine. We need to find the full GenBank
> entry given a particular identifier, unfortunately the
> easiest way I've found so far seems to be the Entrez
> system, and that appears to not be possible to
> download. Is there another way to get the full
> genbank entry given the identifier?
> Jordan Swanson
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Iddo Friedberg, Ph.D.
The Burnham Institute
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