[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.
Hello,
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:
http://www.molbiol.ox.ac.uk/databases/dbsearching/shortsearch.htm
On that page, there is also a link to info at the NCBI about using blast
to search with short sequences:
http://www.ncbi.nlm.nih.gov/BLAST/blast_FAQs.html#Short
Good luck.
Bela
.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
Dr. Bela Tiwari Bioinformatics Officer
OU Bioinformatics Centre
South Parks Road, 01865 (2)75507
Oxford OX1 3RE http://www.molbiol.ox.ac.uk
.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
More information about the BBB
mailing list