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positive selection and gene conversion (Read 2970 times)

silke

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positive selection and gene conversion
Aug 3^rd, 2007 at 7:50am

Dear Sergei,

I would like to determine whether there is evidence for positive selection within a gene family.
However, it is very likely that gene conversion took place. As far as I know,
detecting positive selection when gene conversion is also taking place is tricky, because in such a case the
genes analyzed can not be described by a single phylogeny. I was told that models implemented in HYPHY
can deal with such problems (whereas e.g. PAML cannot deal with this). Since I have never worked with HYPHY,
could you please give me some advice on how to proceed? What kind of analysis could I do? E.g. the PARRIS
selection test?

Thank you very much for your help!

Best,
Silke

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Sergei

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Re: positive selection and gene conversion
Reply #1 - Aug 3^rd, 2007 at 9:03am

Dear Silke,

Firstly, run the GARD screen on your data (Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login) to look for evidence of gene conversion. Take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

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study we did along the same lines.

The NEXUS file with partition information output by GARD can serve as input for the Selection/Recombination standard analyses in HyPhy. Use PARRIS to test for evidence of selection on the gene family as a while, while SLAC/FEL/REL corrected for multiple trees can be used to find sites under selection.

Take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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silke

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Re: positive selection and gene conversion
Reply #2 - Aug 14^th, 2007 at 1:33am

Dear Sergei,

thank you very much for your response and your help!

I have one more question:
My alignment consists of >55 genes and
the online implementation of GARD rejects such files.
Thus, I downloaded HyPhy and tried to run GARD locally
on a Windows PC.
However, I got the following error message:
'This analysis requires an MPI environment to run'.
At this point, I don't really know what to do next.
How do I get GARD to run?

Again, thank you very much for your help in advance.

Best wishes,
Silke

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: positive selection and gene conversion Reply #3 - Aug 14^th, 2007 at 6:34pm Dear Silke, GARD would take too long to run on a single desktop, especially for larger alignment, hence the implementation requires a computer cluster. One possibility is to partition your sequence into groups and then run GARD on each of them. How long (in nucleotide bp) are your alignments? Cheers, Sergei
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silke YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 3	Re: positive selection and gene conversion Reply #4 - Aug 16^th, 2007 at 9:25am Dear Sergei, my alignment is ~ 1000 bp. Cheers, Silke
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: positive selection and gene conversion Reply #5 - Aug 20^th, 2007 at 8:48am Dear Silke, I can run the alignment through GARD on our cluster for you if you'd like; you can send it to me to spond at ucsd dot edu Cheers, Sergei
Back to top	Associate Professor Division of Infectious Diseases Division of Biomedical Informatics School of Medicine University of California San Diego WWW IP Logged

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