which tool to compare two proteomes ?

Question

[guillaume.rbt]

Hi everyone,

I have two proteomes of two strains of the same fungi species. I would like to compare the two fasta files, and find which peptides sequences are similar between the two sets, and which one are specific. I don't know which is the best tool to do that.

Does anyone have any idea? Thanks

[microfuge]

In my experience divergence between strains is high for fungi. Standalone version of inparanoid http://inparanoid.sbc.su.se/cgi-bin/index.cgi should work ok.