Question: How To Compute Dn/Ds Ratio And Get Descriptive Statistics On Thousands Of Sequences ?
gravatar for Bioch'Ti
7.1 years ago by
France (Avignon)
Bioch'Ti980 wrote:

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?


next-gen selection snp statistics • 6.6k views
ADD COMMENTlink modified 4.9 years ago by hadasa1.0k • written 7.1 years ago by Bioch'Ti980

To clarify: You are referring to the ratio of Non-synonymous vs. Synonymous substitution, correct?

ADD REPLYlink written 7.1 years ago by Michael Dondrup41k
gravatar for Dave Lunt
7.1 years ago by
Dave Lunt1.9k
Hull, UK
Dave Lunt1.9k wrote:

You could use BioPerl to do this. Calculating dN:dS can be done in a BioPerl script by running PAML. See this page and slide 76 of this presentation To count the GC there is a script here and to modify it by codon position should be quite possible.

ADD COMMENTlink written 7.1 years ago by Dave Lunt1.9k

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

ADD REPLYlink written 7.1 years ago by Neilfws47k
gravatar for hadasa
7.1 years ago by
hadasa1.0k wrote:

Have a look at HyPhy(Hypothesis testing using Phylogenies). 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.

ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by hadasa1.0k
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