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DEPS (Read 2692 times)
perry
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DEPS
Dec 3rd, 2012 at 5:06am
 
Hello!
Another couple of questions...
As far as I understood, MEME is suitable for detecting diversifying selection, whereas DEPS is devised for directional selection. I noticed that DEPS has been mostly used for studying viral populations. My question is whether it is also suitable for inter-specific comparisons (e.g. To identify residues that evolve under directional selection in a phylogeny of mammalian genes). In this case, how do sites identified with DEPS relate to those identified using methods that do not specifically model directional selection (e.g. PAML M8)?

Thank you so much!
Perry
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konrad
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Re: DEPS
Reply #1 - Dec 4th, 2012 at 1:41am
 
Dear Perry,

Yes, DEPS (and our other tools for finding directional selection) is suitable for inter-specific comparisons. Note that we are using the term "directional selection" in a way that is somewhat non-standard (i.e. directional selection in the phylogenetics context is not quite the same as directional selection in the population genetics context). Here is a description of what is detected by our models of directional selection, from our recent MEDS paper (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login ):

"Among positively selected evolutionary changes, a distinction can be made between diversifying selection, where any nucleotide substitutions that change the amino acid are favored, and directional selection, where only substitutions towards a small number of target amino acids are selected for. Detection of genes or sites evolving under positive selection [1]–[6] has been dominated by methods which explicitly or implicitly assume diversifying positive selection. This assumption allows evolution to be modeled as a continuous-time Markov process without assuming that any particular residue is the preferred target of substitutions at any sites. For most models of diversifying selection, apart from a single rate governing amino acid change, the process is no different from one site to the next. By contrast, models have been proposed in which specific residues do have special status at specific sites. In models of toggling selection [7], substitutions away from a site-specific “wild type” amino acid are likely to be followed by reversions to that amino acid. Models of directional selection [8], [9] allow substitution rates towards a site-specific “target” amino acid to be accelerated. By making a distinction among all possible targets of a substitution, such models allow the detection of positive selection favoring mutations towards one amino acid, even at sites where the overall rate of amino acid change is decreased by purifying selection."

Hope this helps,
Konrad Scheffler
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perry
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Re: DEPS
Reply #2 - Dec 6th, 2012 at 4:00am
 
Yes, thank you very much!
Perry
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