gene structure

Bill_A_Nussbaumer at Bill_A_Nussbaumer at
Thu May 10 16:12:45 EST 2001

What you want could be accomplished by interpreting tblastn results from
the ncbi website (  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

If you need this to be automated you might look into using webblast
( but as
for automatically translating any results into exon boundaries, I don't
know of any (maybe you could ask the folks at

Just a suggestion.

Good Luck,

-Bill Nussbaumer

Sent by:  owner-comp-bio at

To:   bionet-biology-computational at
Subject:  gene structure


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

Jose Pereira-Leal

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