[Bioperl-l] Ks saturation

Roy Chaudhuri roy.chaudhuri at gmail.com
Tue Jun 19 09:48:10 EDT 2012


Hi Subarna,

These are PAML specific questions rather than anything directly related 
to BioPerl (since BioPerl is just acting as a wrapper around codeml), so 
it would be better to ask your question here:
https://www.ucl.ac.uk/discussions/viewforum.php?f=54

Cheers,
Roy.

On 17/06/2012 04:18, subarna thakur wrote:
>
> Dear all,I am trying to calculate dn/ds values of  all
> orthologous gene pair between a pair of genome using pairwsie_kaks.pl
> script within bioperl which evokes the codeml program in runmode -2.
> When I am analyzing the results, some of the genes
> have anomalously high dS or Ks values and some of them even
> reaching more than 100 as a result of which the average value of Ks
> for the whole genome  shots up. These genes are orthologous
> genes and even share more than 50% sequence identity. Should I
> consider these genes for the anlysis or left them out. If I left them
> out, then upto what cutoff value of Ks should I consider for
> analysis. In some papers, I have found that they have considered Ks
> values as high as 5.6. Is there a way for determining the cutoff
> value for Ks? Subarna  
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