The fasts3/tfasts3 programs are designed to do exactly this search - to
search a protein (or translated DNA) database with a set of non-contiguous
peptide fragments.
It is available as part of the fasta3 package
ftp://ftp.virginia.edu/pub/fasta/fasta3.shar.Z
and from the fasta WWW site at:
http://fasta.bioch.virginia.edu/fasta
Bill Pearson
