[BiO BB] Short peptide alignment search

[Dana Gerber]

Hong hi,

Try to restrict your search to SWISS PROT database.
Also i suggest you to search in Blocks database
bioinformatics.weizmann.ac.il/blocks


"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
>
>
>
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board