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Subject: Re: gene structure
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What you want could be accomplished by interpreting tblastn results from
the ncbi website (http://www.ncbi.nlm.nih.gov/BLAST/).  This would blast
your (reverse-translated) protein against a nucleotide database.  Hits
against genomic sequence might then reveal your intron-exon boundaries
while hits against mRNAs should give you clues to 3' and 5' UTRs if you're
interested.

If you need this to be automated you might look into using webblast
(http://www.genet.sickkids.on.ca/bioinfo_resources/software.html) but as
for automatically translating any results into exon boundaries, I don't
know of any (maybe you could ask the folks at www.bioperl.org).

Just a suggestion.

Good Luck,

-Bill Nussbaumer





Sent by:  owner-comp-bio@hgmp.mrc.ac.uk


To:   bionet-biology-computational@net.bio.net
cc:
Subject:  gene structure


Hi!

Does anyone know of any software which given a protein sequence (or a set
of
protein sequences) searches genomic databases and outputs the intron-exon
boundaries for each protein sequence? Software running on Solaris or Win98
would be ideal.

Thanks,
Jose Pereira-Leal







.