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ASR (Read 2230 times)
Kartik Sunagar
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ASR
May 10th, 2011 at 11:16am
 
Dear all,

I am new to this. I am using the ASR algorithm to reconstruct ancestral sequences. I wanted to know, out of the three types of sequences generated by the program (marginal, joint and sampled), which is the most reliable one? Does this solely depend on the support values for each type? Can I rely on these sequences to evaluate the selection regimes for the particular clade the sequence represents?

Thank you very much,
Kartik
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Sergei
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Re: ASR
Reply #1 - May 11th, 2011 at 11:23am
 
Hi Kartik,

Take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login for some discussion. You should NOT use ancestral sequences to infer anything about selection -- there are dedicated methods for doing that (SLAC/FEL/REL etc).

Sergei
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Kartik Sunagar
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Re: ASR
Reply #2 - May 11th, 2011 at 2:02pm
 
Dear Sir,

Thank you very much for the reply.

What I meant was, I wanted to construct a homology model for the ancestral sequences and infer the sites/domains under selection so that I could compare it with the extant proteins. Is that inappropriate?

Thank you very much,
Kartik  Smiley
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Sergei
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Re: ASR
Reply #3 - May 12th, 2011 at 1:08pm
 
Hi Kartik,

Sure, for simply mapping which substitutions happened along which lineages, ASR is fine (use the joint mode for that).

Sergei
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Division of Biomedical Informatics
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Kartik Sunagar
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Re: ASR
Reply #4 - May 13th, 2011 at 2:14pm
 
Thank you for the help.

Best,
Kartik
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