Protein mapping

[anawang]

Hi all,

Does anyone know of pathway/function mapping tools for proteins analogous to those that exist for next gen sequencing? Any programs for proteins analogous to the likes of Maq/Soap/Bowtie/etc?

I am trying to analyze mass spec data of peptides about 10-20 amino acids long that have been matched to proteins.
Ideally, the program will allow us to search large numbers of proteins at once across many databases, as these proteins can be from any of thousands of species of bacteria.

Are there short read aligning programs for protein sequences?

Any suggestions/advice would be greatly appreciated - thanks!

[Richard Finney]

blat can align protein sequences
Use the -t=prot and -q=prot parameters for protein on protein search.
You can also search for protein sequence on dna sequence (with different parameters).