Question: Finding Significant Amino Acid Changes Between Species
0
gravatar for Alex
18 months ago by
Alex0
Alex0 wrote:

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.

gene sequence alignment genome • 343 views
ADD COMMENTlink written 18 months ago by Alex0

What do you mean by significant?

You want to find all non-synonymous changes in every protein?

ADD REPLYlink written 18 months ago by Joe18k

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?

ADD REPLYlink written 18 months ago by Alex0
1

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.

ADD REPLYlink written 18 months ago by Joe18k

I'm hoping to find changes in proteins that may contribute to the difference in lifespans between these species.

ADD REPLYlink written 18 months ago by Alex0
1

So you want to do a quantitative association study (for lifespan) by comparing only 1-vs-1? How do you think that would work?

ADD REPLYlink written 18 months ago by WouterDeCoster45k

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.

ADD REPLYlink written 18 months ago by Joe18k

Of course. Thank you for your help.

ADD REPLYlink written 18 months ago by Alex0

What do you mean by significant?

You want to find all non-synonymous changes in every protein?

ADD REPLYlink written 18 months ago by WouterDeCoster45k

Yes, I want to find protein pairs with non-synonymous changes.

ADD REPLYlink modified 18 months ago • written 18 months ago by Alex0
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