BLASTing short sequences: try Blitz

Arnoud van Vliet avvliet at knoware.nl
Mon May 24 08:00:07 EST 1999

Dear Mathieu

you could try Blitz, at the EBI site (www.ebi.ac.uk). I don't know why, but
it has worked better for me than Fasta or Blast with a 10 AA sequence. Only
Blitz gave me a decent homology, with what later turned out to be the right
homologue of our protein.

I'll leave it to the specialists to explain why.

Hope this helps

Mathieu Ingouff wrote in message <37455A10.AF56A7B1 at sgen.slu.se>...
>Hi netters,
>I have a couple of protein sequences that are quite short  <20 AA, so
>when i blast it, it is not always nice
>Is there any reliable software similar to BLAST-p function that can work
>with short sequences?
>Thank you
>  Mathieu Ingouff, PhD student
>  SLU, Department of  Forest Genetics
>  Genetikvagen 1B, Box 7027
>  S-750 07 Uppsala, Sweden
>  email: mathieu.ingouff at sgen.slu.se
>  fax: +
> phone: +

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