Database search with multiple unordered peptide sequences?

David Mathog mathog at
Thu Jun 11 16:07:00 EST 1992

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 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
manager, sequence analysis facility, biology division, Caltech

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