Question: How To Compute Dn/Ds Ratio And Get Descriptive Statistics On Thousands Of Sequences ?
3
gravatar for Bioch'Ti
4.0 years ago by
Bioch'Ti840
France (Avignon)
Bioch'Ti840 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?

Cheers

ADD COMMENTlink modified 21 months ago by hadasa930 • written 4.0 years ago by Bioch'Ti840
1

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

ADD REPLYlink written 4.0 years ago by Michael Dondrup27k
3
gravatar for Dave Lunt
4.0 years ago by
Dave Lunt1.7k
Hull, UK
Dave Lunt1.7k wrote:

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.

ADD COMMENTlink written 4.0 years ago by Dave Lunt1.7k

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

ADD REPLYlink written 4.0 years ago by Neilfws41k
3
gravatar for hadasa
4.0 years ago by
hadasa930
hadasa930 wrote:

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.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by hadasa930
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