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I would be interested to know if there is a method/analysis or a set of methods to compare two groups of pathways or families of proteins.

I would specifically be interested by a system biology approach which takes all the components of the pathway or family of proteins. I would like to know if there is a method which can not only compare the similarity, homology, divergence and convergence of a family of proteins (like ribosomal proteins) between species but also between groups in the same organism.

For example I would like to compare the molecular components of vesicular trafficking pathways to the molecular components of non-vesicular pathway in the same organism saccharomyces cerevisiae (yeast).

I would greatly appreciate your suggestions.

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I am not sure that I completely understand, it would be a little easier if you described the problem you are trying to solve or what the motivation is.

However, I think that some of what you want to do can be accomplished by inferring gene/protein trees for each gene/protein of interest across different species (including paralogs, maybe?). This will allow you to see discordance or correlation of evolutionary rates of different genes/proteins across species.

THis kind of analysis is built into HyPhy, though I have never used it. There are also somewhat less involved methods for measuring distances between trees.

You might also be interested in protein co-evolution methods, depending on the question at hand.

Your mentioning systems biology methods suggests that you have something rather different in mind, as none of these things I suggest are really systems biology IMO, but I'm not sure what it would be. Possibly you are interested in integrating e.g. protein-protein interaction or metabolic network information as well, but that would probably involve something more homebrewed that might integrate some of these things.

Hope that helps.

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