How to calculate Ka/Ks ratios

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timpanister
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How to calculate Ka/Ks ratios

Post by timpanister » Sun Mar 23, 2008 9:40 am

Hi,

Can Ka/Ks ratio be calculated for within species ie polymorphism data?

Cat
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Post by Cat » Tue Mar 25, 2008 6:31 pm

For a few cases maybe, but probably not for most. Ka is the number of non-synonymous base changes and Ks is the number of synonymous base changes in the same gene. In most cases of within species gene polymorphism no synonymous base changes present (say Ka=1 and Ks= 0, then ratio is 1/0, which cannot be).

liquidkodak
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Re: How to calculate Ka/Ks ratios

Post by liquidkodak » Thu Oct 23, 2008 5:54 pm

I don't know if you are still checking this board but you can use Ka/Ks for intraspecies comparisons. Here is the paper that developed the idea. Hughes AL, Nei M. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167-170.

zz63
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Re: How to calculate Ka/Ks ratios

Post by zz63 » Fri Oct 31, 2008 9:02 pm

The software, KaKs_Calculator, can do this. It contains several existing methods and can be found at http://www.yale.edu/townsend/software.html

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