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Sliding windows to show individual codons under selection (Read 1819 times)
DanniUEA
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Curious HyPhy user

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Sliding windows to show individual codons under selection
Sep 11th, 2013 at 7:32am
 
Hi
I was wondering if it is possible, using the DataMonkey site, to carry out calculations of dn/ds using a sliding window? i.e. looking across several (of the same gene) sequences for a number of closely-related species, and measuring dn/ds for each codon going in one direction, and flagging up individual codons inferred to be under selection (be it positive or purifying). I know this has been done with MHC genes with regards to genes that encode peptide-binding regions, and I am also working with an immune gene group. Any advice would be great,
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Sergei
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Datamonkeys are forever...

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Re: Sliding windows to show individual codons under selection
Reply #1 - Sep 11th, 2013 at 10:47am
 
Hi Danni,

I am afraid I don't understand what you are after with this analysis. What are you trying to detect, exactly?  If you want codon level resolution, you already get this with Datamonkey. If you want to pre-partion the sequences into regions based on external considerations (e.g. structure or function) and compare their average dN/dS, then you will need to perform the analysis in HyPhy (datamonkey doesn't support the analysis). There are some examples of how to do it in section 2.7.2  of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login.

Sergei
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