[BiO BB] Short peptide alignment search
H. You
youhg at email.uc.edu
Tue Dec 4 17:01:19 EST 2001
Hi,
I have a short peptide (~ 5 - 8 amino acids). I used BLAST (actually the
tblastn) to search the alignment in the "nr" database. The expect value
was set at 10000 and word size is 2. The matrix used is PAM30. I usually
get either no matches or more than a hundred matches. It is real time
consuming to go through all the matches. In textbooks or tutorials,
protein alignment with long sequence is usually discussed. My question is
what is the strategy to conduct an alignment search with a protein
of short sequence. I hope that I can get some help from veterans in this
field.
Thanks.
Hong
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