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4.8 years ago
Alex
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0
I'm trying to compare two mammalian genomes, one from species A and another from species B. I'd like to find significant amino acid changes between orthologous proteins in the protein sequences of A and B. What is the best way of accomplishing this task? I've looked into programs like MAFFT and OMA, but I haven't figured it out yet. Thanks.
What do you mean by significant?
You want to find all non-synonymous changes in every protein?
If I was to run OMA to find all orthologous pairs of proteins, can I filter pairs that contain non-synonymous changes? Is it worthwhile?
You could, in principle, use any orthologue clustering tool. You'll need to decide what you do with unique proteins. Remember that you will also get groups that contain more than just 2 proteins, so you need to consider how you handle these too - for instance, are you interested in every site that varies in every cluster, or just in some percentage of clusters (i.e. frequent mutations).
I don't know whether this is worthwhile, because I don't know what your biological question is.
I'm hoping to find changes in proteins that may contribute to the difference in lifespans between these species.
So you want to do a quantitative association study (for lifespan) by comparing only 1-vs-1? How do you think that would work?
This is probably an OK place to start, but concluding something like that from this alone will be a hell of a stretch.
From what little I know of aging genetics/genomics, there's a lot to be said for non-genic changes such as telomere shortening, epigenetic mechanisms, etc.
It'll be an interesting study, but I don't know that you'll get a convincing outcome from this alone for your question.
Of course. Thank you for your help.
Yes, I want to find protein pairs with non-synonymous changes.