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
