Dear community,
I have some CDS from different species for a specific gene, nicely aligned in a fasta file. Since my interest is to analyze non-synonimous mutations between those species, I would like to create a table containing which aminoacidic position is varying from the refseq in which species, and the nature of that variation (e.g. C>S). If possible, I should also annotate which bases are changed in the codon for each nonsynonimous mutation. That task might be done manually, but I'm positive that there must be some good-hearted, time-saving way to do it by using software. Does this ring a bell?
Thanks and greetings to everybody.
Hi,
You should try this:
https://code.google.com/p/kaks-calculator/
http://www.datamonkey.org
UPDATE: One of my labmates almost achieved to do the task using Geneious. Not free, not exactly what we were trying to do (it'll need some manual editing) but I guess it's our best shot so far.
Antony, I really appreciate your suggestions! Currently I'm diving into what Datamonkey does and I find it quite useful. As for the Kaks calculator, I haven't tried it yet but I'll give it a chance for sure - I'm positive that I can do some interesting stuff with it. Thanks!
No pre-built software that I am aware of. Know anyone good at scripting? :)
Try using R packages like "pegas" or "ape" https://cran.r-project.org/. They can read fasta sequences and have functions to summarize variable positions.
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