[BiO BB] Short peptide alignment search

Bela Tiwari btiwari at molbiol.ox.ac.uk
Wed Dec 5 05:17:24 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.


We have a web page that has a couple of hints on searching with short
sequences, although its not  complete! (I will be taking notes on any
advice  sent in answer to your question...)

The page is at:


On  that page, there is also a link to info at the NCBI about using blast
to search  with short sequences:


Good luck.


Dr. Bela Tiwari                Bioinformatics Officer
OU Bioinformatics Centre          
South Parks Road,                  01865 (2)75507 
Oxford  OX1 3RE               http://www.molbiol.ox.ac.uk

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