Prediction Tool for Antigenic Peptides?

[Allison]

WS wrote:
> 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

Current Protocols in Immunology (unit 9.20 has a nice overview of making 
peptides for immunization. They suggest 10-15 aa long.

Also, try the invitrogen site again.  It was working for me just now.

HTH
Allison