Constructing the ancestral state of amino acid
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Entering edit mode
7.2 years ago
RT ▴ 360

Hello Everyone,

I have the results from codeml analysis where I have identified few sites that are under positive selection in my target species. I am now looking for the change in amino acid in the nearest species and the ancestral amino acid. I have around 20 such genes where I have identified positive selection in orthologs of these genes. I can easily identify the amino acid in nearest species from the MSA of these genes. I am wondering if it is fair enough to identify the ancestral amino acid same way- looking at MSA for amino acid in the distant species retained in the orthology cluster. or there is any other way to construct the ancestral state of these sites?

I hope I am clear in asking the question.

Thanks.

paml codeml selection • 1.8k views
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Entering edit mode
7.1 years ago
Juke34 ★ 7.1k

You could try from the DNA sequence using the Ortheus tool. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577868/). It allows to reconstruct the ancestral state of DNA sequences aligned. 

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Entering edit mode
7.1 years ago

FastML http://fastml.tau.ac.il/http://nar.oxfordjournals.org/content/40/W1/W580.long is a web server for ancestral sequence reconstruction, using the sequence MSA plus phylogenetic tree as input. I don't know if that answers your question, but I have seen papers that use both PAML and FastML and compare the results.

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