BLASTing short sequences

Bernard P. Murray, PhD bpmurray*STUFFER* at socrates.ucsf.edu
Fri May 21 18:29:33 EST 1999

In article <37455A10.AF56A7B1 at sgen.slu.se>, Mathieu.Ingouff at sgen.slu.se wrote:

> 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
> Mat

What do you mean "not nice"?  If you mean that you are not getting
any hits you have to change some of the defaults (especially
the "expected" value) for the search.  Read the documentation as
this has much useful information.
     I hope that this helps,
Bernard P. Murray, PhD
Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA

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