[BiO BB] Is it possible to Blast against genBank files

Boris Steipe boris.steipe at utoronto.ca
Thu Dec 18 17:01:20 EST 2003

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)?
> > blast automatically
> > 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

Yes, you can get the files through the SeqHound remote Perl API - easy to
program and no blacklists.

See:            <http://blueprint.org/seqhound/seqhound.html>
and especially: <http://blueprint.org/seqhound/api_help/apifunctslist.html>

Best regards,


Boris Steipe
University of Toronto
Program in Proteomics & Bioinformatics
Departments of Biochemistry & Molecular and Medical Genetics

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