I am interested in finding any homologs to a protein I am working on, however, I have only an N-terminal sequence of about 15 amino acids, and 3 internal peptides from tryptic digests. I have used the default scoring matrices, gap existence & extension penalties, and word sizes for the NCBI blastp web interface as well as for the 'search short nearly exact matches' using the blastcl3 client-server interface : ../blastcl3 -p blastp -e 10 -d swissprot -F T -T T -M BLOSUM62 -G 11 -E 1 -W 3 ../blastcl3 -p blastp -e 10 -d nr -F T -T T -M BLOSUM62 -G 11 -E 1 -W 3 ../blastcl3 -p blastp -e 20000 -d swissprot -F F -T T -M PAM30 -G 9 -E 1 -W 2 ../blastcl3 -p blastp -e 20000 -d nr -F F -T T -M PAM30 -G 9 -E 1 -W 2 Although many 'hits' were returned, none had e-values less than 0.1. What is the threshold for 'significance' with such short peptides? Is there a preferred method to find homologs when dealing with these short fragments? Cheers, Tristan -- Tristan J. Fiedler, Ph.D. Postdoctoral Research Fellow - Walsh Laboratory NIEHS Marine & Freshwater Biomedical Sciences Center Rosenstiel School of Marine & Atmospheric Sciences University of Miami tfiedler at rsmas.miami.edu t.fiedler at umiami.edu (alias) 305-361-4626