DB searching with short peptides from phage display

William R. Pearson wrp at alpha0.bioch.virginia.edu
Mon Aug 13 04:22:19 EST 2001

For short peptides, you need to be certain to use a "shallow" scoring matrix.

FASTA with ktup=1 and "-s M10" or "-s M20" can reliably identify sequences
that are 70% - 85% identical given 10 - 15 residues of sequence.

Bill Pearson

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