Prediction Tool for Antigenic Peptides?

WS via methods%40net.bio.net (by novalidaddress from nurfuerspam.de)
Thu Jun 10 08:08:30 EST 2010


Dear Experts,

I plan to order some custom peptide antibodies. While I have found a
useful resource to estimate the antigenicity of peptide sequences,
Antheprot (http://antheprot-pbil.ibcp.fr/), I wonder if there is a
tool that I can use to check whether a selected sequence is present
somewhere else in the species' proteome. Of course, one may BLAST each
possible peptide manually, but maybe there's an automated solution? I
have come across http://peptideselect.invitrogen.com/peptide/index.jsp,
unfortunately, it seems not to be functional (Opensuse 11.1 / Firefox
3.5.9 or W2KSP4 in a VirtualBox).

Another question: How many AA is most appropriate?

Thanks for your help!

Wo


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