For short peptide sequences I would recommend that you try SCANPS by Goeff
Barton. You can submit your sequences at the following web site.
http://www.ebi.ac.uk/scanps/
or alternatively you could try Edinburgh Biocomputing Systems´ very fast
implementation of the true Smith and Waterman algorithm called MPsrch at
http://www.ebi.ac.uk/MPsrch/
All the best for your research.
"Darek Kedra" <darked at my-deja.com> wrote in message
news:a85419e1.0108081541.446f7d16 at posting.google.com...
> Dear All,
>> I've got short, 9-15 AA long peptide sequences from phage display.
> These are "random" sequences which happen to interact with a target.
> The next step is to find if something similar exist in nature.
> I wonder if you can recommend "the best" program/algoritm for doing
> it.
> I've used blast (blastp / nr database and tblastn / est db) but
> finding anything meaningful in 500+ weak matches is a tall order.
>> Thank you in advance.
> Greetings
>> Darek Kedra
>> d a r k e d at m y -d e j a . c o m
>> ---
>
