[Bioperl-l] Ks saturation

subarna thakur bubli_thakur at rediffmail.com
Sat Jun 16 23:18:56 EDT 2012

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?

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