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dN and dS values from Datamonkey (Read 3286 times)
mattn
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dN and dS values from Datamonkey
Jul 2nd, 2008 at 6:40pm  
Hi!

I have two questions, which I hope are easy to answer:

1. Is it possible to use Datamonkey to get a global estimate of dN or dS alone?  I noticed that SLAC and REL report a global dN/dS, but I would like to know the values of dN and dS because I want to know if the rate of synonymous substitution varies over different parts of the molecule (e.g., does the extracellular domain have more synonymous mutations than the cytoplasmic domain).  Is there a better way to ask this question?

2. With a data set of 17 sequences, is 0.1 an appropriate significance cutoff for SLAC and FEL?

Thanks for your help!

Matt
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Sergei
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Re: dN and dS values from Datamonkey
Reply #1 - Jul 2nd, 2008 at 10:17pm  
Dear Matt,

1. Both SLAC and REL report a site-by-site table (click on the [HTML] or [CSV] links in the Reports section), e.g. Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login that includes dS and dN estimates for each site. Is that what you had in mind? You can plot the results as well to obtain an idea of spatial rate variability, e.g. as in the attached image.



If you want to compare synonymous rates over regions (as opposed to individual sites) you are probably better off doing a relative-ratio type test on synonymous rates between partitions (see Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login for an HIV case).

2. Should be appropriate. The tests tend to be quite conservative (Type I error rate < specified p-value).

Cheers,
Sergei
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mattn
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Re: dN and dS values from Datamonkey
Reply #2 - Jul 3rd, 2008 at 6:38am  
Dear Sergei,

Thanks!  The idea of plotting the dN and dS for each site is a great one.  I am still curious about how SLAC and REL arrive at global estimates for dN/dS.  Is it just a simple mean of the dN/dS ratio at each site, or is there something else taken into consideration?

Thanks,

Matt
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Sergei
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Re: dN and dS values from Datamonkey
Reply #3 - Jul 3rd, 2008 at 9:00am  
Dear Matt,

SLAC estimates mean dN/dS directly by ML (single parameter shared by all sites). This is needed for ancestral state recovery and mutation mapping. REL estimates a distribution of dN/dS (with 3 classes for dN and 3 for dS) from the entire distribution and reports the mean of this distribution. In neither case are site-specific rates involved in obtaining the mean.

Cheers,
Sergei
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