Computing ka/ks ratio for individual genes.

Question

[Shakunthala Natarajan]

Hello. I am trying to find ka/ks ratios for some duplicated genes in a genome. I have two gene duplicate groups - [g1,g2], a tandem duplicate pair and [g2,g6], a proximal duplicate pair. I use KaKs_Calculator to obtain ka/ks ratios between gene pairs. Lets say I get a ka/ks value of 0.4 for the gene pair g1,g2, and a value of 1.2 for the pair g2-g6. I would like to find what's the selection pressure operating on an individual gene in this group. g2 is present in both the groups. How can I compute the individual ka/ks value on an individual gene basis after these pairwise calculations? It would be great if someone could help me out! Thank you!

Answer 1

[shelkmike]

It's better to use PAML to calculate Ka/Ks. With PAML, you can use the so-called "branch model", which allows you to calculate Ka/Ks for each branch of a phylogenetic tree of the gene family. Probably, this is what you need. (also, in PAML, "Ka/Ks" is called "dN/dS", or, alternatively, "omega". These are all synonyms)

[Shakunthala Natarajan]

Hi. Thank you. I will look into PAML.