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I have a list of candidate proteins as the result of my analysis. I am now trying to find various characteristics that they have in common. One of the things I would like to check is if my candidates are evolving faster or slower than the rest of the proteins in my dataset.

Now, I know how to do this manually by building multi species alignments for each of my proteins and calculating ka/ks ratios for each set of alignments. This, however, is not a trivial process and I really do not want to do this manually for my ~1500 candidates.

Can anyone suggest a tool that will take two lists of proteins and return an estimate of evolutionary rate for each one?

I am primarily interested in human but also mouse, yeast, fly and worm. Ideally, I would need a tool that can take a list of proteins, assign them to an orthologous group and return a value representing the rate of evolution for that group.

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I think you'll have to build the MSA regardless of the strategy that you use. You could try faster tree-based methods. – bobthejoe Nov 21 '12 at 19:59
are you working on species that have already been sequenced (for which you might info in databases), or do you have novel sequencing data? – Michael Kuhn Nov 22 '12 at 8:56
@MichaelKuhn definately sequenced. I am working on human primarily. There should be a database around that can give me this information right? – terdon Nov 22 '12 at 10:10
The eggNOG database also contains alignments for protein families, but these are on the amino acid level. So you would still somehow have to go back to a nucleotide alignment, which I'm not quite sure how to do. :-/ Might be a good question to ask on BioStar with its larger bioinf audience. – Michael Kuhn Nov 22 '12 at 11:01
@MichaelKuhn, protein data is fine, I just realized my original question was not clear enough and have updated it. I said genes in the original because I thought it would be easier to find a relevant tool. My bad. – terdon Nov 22 '12 at 11:23

If protein alignments are sufficient for you, I suggest that you look at the eggNOG database. There you can download mappings from proteins to protein families, and for the families you can also download pre-computed multiple (protein) sequence alignments.

I guess depending on the type of analysis you want to do you would have to trim the alignments to get only homologous regions (for example, see this recent paper[1]).

  1. Wu M, Chatterji S, Eisen JA. 2012. Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7(1): e30288, doi:10.1371/journal.pone.0030288.
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