[BiO BB] Short peptide alignment search

H. You youhg at email.uc.edu
Tue Dec 4 17:01:19 EST 2001


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 




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