[BiO BB] Short peptide alignment search

Dana Gerber danag at bioinformatics.weizmann.ac.il
Wed Dec 5 04:11:47 EST 2001

Hong hi,

Try to restrict your search to SWISS PROT database.
Also i suggest you to search in Blocks database

"H. You" wrote:

> 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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