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