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
