HyPhy message board - Interpreting SLAC results

	Welcome, Guest. Please Login

Home

Help

HyPhy message board › Methodology Questions › How to › Interpreting SLAC results

(Moderators: Sergei, Simon)

‹ Previous Topic | Next Topic ›

Pages: 1

Send Topic

Interpreting SLAC results (Read 2047 times)

audrinab

YaBB Newbies

Offline

Feed your monkey!

Posts: 1

Interpreting SLAC results
Apr 24^th, 2010 at 7:21pm

Hi,
I have performed a SLAC analysis on a dataset of 80 viral sequences to detect positive selection and I am trying to interpret the results. I got a mean dn/ds of 0.4, which indicates purifying selection. However I got several codons with signals of positive selection.
How can I explain the different results? How is the mean dn/ds calculated? Is it an average of all dn/ds values of each codon in the alignment?

Thanks a lot for any help in this matter.

IP Logged

Sergei

YaBB Administrator

Offline

Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male

Re: Interpreting SLAC results
Reply #1 - Apr 26^th, 2010 at 7:15am

Dear audrinab,

Your question is difficult to answer concisely and informatively. There is no inconsistency in the report that MEAN dn/ds (the entire gene) is < 1, while for some sites it is >1. There is no direct relation between the mean dN/dS reported by SLAC (based on maximum likelihood) and site-by-site estimates of dN/dS (inferred using counting heuristics. Loosely, the mean of SLAC dN/dS (by site) should be similar to the reported mean dN/dS, but the exact relationship is non-trivial. Please refer to our selection detection book chapter (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

WWW

IP Logged

Pages: 1

Send Topic

‹ Previous Topic | Next Topic ›

« Home

‹ Board

Top of this page