Database search with multiple unordered peptide sequences?
wrp at cyclops.micr.Virginia.EDU
Fri Jun 12 09:42:56 EST 1992
FASTA is well-suited to searching with unordered fragments - simply
search with each permutation of the fragments and look at the "initn" score.
In the example cited (61-70 + 100-110 + 151-160), the initn score should
combine the scores for each peptide (minus a penalty for each gap). Thus,
you should see a score that looks like this:
initn init1 opt
>white locus 88 40 40
(assuming each set of 10 residues had a perfect match score of 40)
It is true that fasta does not show the alignment that gives rise to
the 88 score, but that can be done with "lfasta".
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