Database search with mul

Brett Lindenbach Brett_Lindenbach at QMS1.LIFE.UIUC.EDU
Fri Jun 12 11:13:21 EST 1992

        Reply to:   RE>Database search with multip
Why not try BLAST? It is my understanding that this program (Basic
Local Alignment Search Tool) is particularly useful for finding matches
between small peptide stretches.

Date: 6/11/92 5:07 PM
To: Brett Lindenbach
From: David Mathog
Situation:  you have multiple peptide sequences _from the same 
protein_ , but their order is not known.  Each sequence is short (say
6-10 aa).  What database search tool, if any, can accept this sort of

I already did a trial run with the Drosophila white gene, where I took
three peptide chunks and made one test sequence out of them (like 61-70
101-110 + 151-160 = sequence, although I don't recall the exact
I ran this through Genbank's FASTA, but it only matched the best
and did not align (with gaps) the other two.  I sent the same thing to
BLAZE, but it hasn't answered yet, so no info on that.

Any suggestions?

David Mathog
mathog at seqvax.caltech.edu
manager, sequence analysis facility, biology division, Caltech

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From: mathog at seqvax.bio.caltech.edu (David Mathog)
Subject: Database search with multiple unordered peptide sequences?
Date: 11 Jun 92 21:07:00 GMT
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