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HYPHY Package >> HyPhy feedback >> Multiple methods and the FUBAR paper http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1364305698 Message started by Day on Mar 26th, 2013 at 6:48am |
Title: Multiple methods and the FUBAR paper Post by Day on Mar 26th, 2013 at 6:48am
Hi there,
I'm trying to ascertain which would be the best method(s) for trying to find positively selected sites from a small number of MHC Class I exon 3 sequences (2 species together, n=26 (10 of species 1 and 16 of species 2). I am currently just running REL, MEME and FUBAR and hoping to get some congruence between them. I've read that REL is good for small sample sizes and the site seems to strongly recommend using MEME and FUBAR anyway as they are quite encompassing techniques. However, you might have guessed I'm incredibly new to this - any suggestions would be very helpful indeed! I was hoping to be able to read up about the FUBAR method but my university does not provide access to Molecular Biology and Evolution journal, so not sure if it would be relevant in my situation? Many thanks, Day |
Title: Re: Multiple methods and the FUBAR paper Post by Day on Mar 27th, 2013 at 11:11am
Hi Konrad,
Thank you very much for your helpful response. I am concerned I might have misunderstood how I am able to identify positively selected sites; I have read a few papers that used datamonkey's REL & FEL methods etc to infer PSS by analysing sequences aligned from across species 4 or so species. I thought by including two different but related species I would avoid the problems highlighted in Kryazhimskiy & Plotkin's paper? I guess the sensible solution to finding PSS in my species would thus be to use both MEME and FUBAR (and look for congruence) and look across a broader group of species (there's 8 or so species now with available genetic info)? Many thanks again. I'm slowly trying to unravel the mysteries of it all. Kind regards, Day |
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