How to Compute dN/dS ratio and get descriptive statistics on thousands of sequences ?

Question: How to Compute dN/dS ratio and get descriptive statistics on thousands of sequences ?

Hi Guys,

I'm looking for the best way to (1) compute dN/dS ratios on thousands couples of sequences and (2) get descriptive statistics on these thousands of sequences (length, GC3, etc...) at the same time?

What are the software available to perform that job?

Cheers

created 3.1 years ago by Bioch'Ti 780•3•12

updated 10 months ago by ninia

To clarify: http://en.wikipedia.org/wiki/Ka/Ks_ratio You are referring to the ratio of Non-synonymous vs. Synonymous substitution, correct?

2 answers

You could use BioPerl to do this. Calculating dN:dS can be done in a BioPerl script by running PAML. See this page http://www.bioperl.org/wiki/HOWTO:PAML and slide 76 of this presentation http://jason.open-bio.org/Bioperl_Tutorials/ISMB2007/. To count the GC there is a script here http://www.bioperl.org/wiki/Bioperl_scripts#SeqStats and to modify it by codon position should be quite possible.

created 3.1 years ago by Dave Lunt 1,700•3•11

Or indeed, any of the Bio* projects: they all are well suited to building simple sequence analysis pipelines for many sequences.

Have a look at HyPhy(Hypothesis testing using Phylogenies). http://www.datam0nk3y.org/hyphy/doku.php It has a specilized module for Positive and negative selection detection and which can be relevant to what you want to accomplish for a large dataset of sequences It might help you out.

created 3.1 years ago by ninia 880•2•7

updated 3.1 years ago by ninia