You could try scanps at EBI. The default statistics in the
program tend to promote high scoring short alignments.
This might do what you need.
PS. Best to access through the 'Tools' menu of the newly re-designed
EBI www site.
Mathieu Ingouff 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
> 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: +126.96.36.199.79.
> phone: +188.8.131.52.32.
Dr Geoff. Barton, EMBL-European Bioinformatics Institute, Genome Campus,
Hinxton, Cambs CB10 1SD, U.K., mailto:geoff at ebi.ac.ukhttp://barton.ebi.ac.uk, Tel: +44 1223 494414, Fax: +44 1223 494496