We annotate exome variants with conservation status using sources like PhyloP, GERP but these query the nucleotide instead of the amino acid. As the nucleotide may not be conserved among species, but the amino acid can be we would like to annotate our variants with amino acid level conservation. What database/UCSC track/reqource we can use to annotate this data into our variants? Thanks
You might want to look at several methods, such as SIFT, that use amino acid conservation to predict the effects of a change. This isn't a direct answer to your question, but I'm just guessing that the reason you want AA conservation is to help prioritize variants with respect to likely biological impace.
Hi, Biomed, I assume you work with human data, am I right?
Try PhylomeDB - they provide Maximum likelihood trees and alignments for all human proteins using various species scopes. And yes, all is protein orientated. But you would need to calculated conservation score yourself. I did similar stuff for yeast SNPs, in order to prioritise wet experiments to nonsynonymous SNPs in highly conserved sites. Let me know if you are interested, I can help you with that.