Question: dN/dS ratio (omega)
0
gravatar for dav
13 months ago by
dav0
Belgium
dav0 wrote:

So, I have a group of genes (proteins) - that arent necesarely related and I am interested in dn/ds ratio, or rather the conservation . They are all from the same species (A.thaliana) and I have data on around 600 individuals (mostly from 1001genomes).

What software should I stick to?

I was thinking of PAML (Phylogenetic Analysis by Maximum Likelihood) , more specifically codeml. I would give it aligned sequences, so 600 sequences of the same protein and a tree that goes with it, but I saw people say it is best suited for more distant species.

Is my approach wrong? What should I stick to for this?

ADD COMMENTlink modified 13 months ago by natasha.sernova2.4k • written 13 months ago by dav0
1

if they ar not related (i.e. not homologous) you CANNOT use phylogenetic based methods

ADD REPLYlink written 13 months ago by Whetting1.4k
3
gravatar for natasha.sernova
13 months ago by
natasha.sernova2.4k
natasha.sernova2.4k wrote:

You are on the correct track, but PAML description is very hard.

This is the manual.

http://abacus.gene.ucl.ac.uk/software/pamlDOC.pdf

I would recommend to read all about codeml program (pp. from 28th to 38th.). You will understand what these parameters represent and all that is necessary to specify to run PAML.
I suggest using runmode = -2. What this mode means is described on p. 34.

Good luck!

Natasha

ADD COMMENTlink written 13 months ago by natasha.sernova2.4k

ah, so runmode=-2 gives me the exact lineage ratio I need!

Thank you a lot!

ADD REPLYlink written 13 months ago by dav0

but wait , if I run it pairwise , (runmode -2) , then it compares all sequences to the first one?
or will it compare 3rd to 2nd , 4th to 3rd etc?

Should I leave runmode = 0 to get it globaly?

ADD REPLYlink written 13 months ago by dav0
0
gravatar for natasha.sernova
13 months ago by
natasha.sernova2.4k
natasha.sernova2.4k wrote:

Dear dav,

I think the first url contains the answer to your question about Dn/Ds for a global alignment.

A: Orthologous Genes And Dn/Ds Ratio

The file below is about runmode-option:

http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-877j-computational-evolutionary-biology-fall-2005/labs/pamldescription.pdf

In any case, PAML is a very complicated program as well as its manual.

Below there are a manual how to read PAML-description and other useful urls

– PAML is not an obvious program at all.

http://abacus.gene.ucl.ac.uk/software/pamlFAQs.pdf

http://www.bioperl.org/wiki/HOWTO:PAML

A: How Can I Compare Rates Of Evolution For Two Sets Of Genes?

How To Compute Dn/Ds Ratio And Get Descriptive Statistics On Thousands Of Sequences ?

Good luck!

Natasha

ADD COMMENTlink modified 13 months ago • written 13 months ago by natasha.sernova2.4k
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