Database search with multiple unordered peptide sequences?

Bill Pearson 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".

Bill Pearson

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