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
data?

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
numbers). 
I ran this through Genbank's FASTA, but it only matched the best
subregion
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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