I find that I have a long list of protein accession codes (from rats and humans) that I want to compare to see what is common in each group. What I want to do is convert the rat accession codes to the homologous, or identical, human sequence (or vice versa). Since I have many thousands of codes I want to automate the process and be as accurate as possible. Clearly, there will be some proteins that are not found in both species, but most should have near identical, or near-homologues, in each species.
Does anyone have an easy way of doing this? I'm open to all operating systems and web applications.
Thanks,
Peter
Hi Peter, as Alberto mentioned, there are many databases that can do the work. Two tips may be you are interested. 1) 1-to-1 human-mouse orthologs are ~15000. I guess human-rat orthologs would be similar. 2) If you have problem with ID conversion, you can try a R package named BiomaRt (see http://www.bioconductor.org/packages/2.12/bioc/html/biomaRt.html).
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