sequence input for doing ka/ks analysis

Question

[teesnadi]

Hello

could anybody help me to put the sequence for doing ka/ks analysis? which sequence to put in the input of ka/ks calculator? whether is it only coding sequence of the Genes or the complete Gene sequence? only DNA sequence will be sufficient to predict the synonymous and non-synonymous polymorphism? is it not needed to put amino acid sequence there?

thanks

Teesta

Answer 1

[romain.lannes]

I apologize for this short answers but I am not sure of certain point, I never use it, so I will talk only about what I know:

KaKsCalculator take DNA coding sequence,

To compute Ka and Ks it works on codon, so the sequence have to be aligned at the protein level and to be the same length. KaKsCalculator remove gap but I don't know how it does and so if the input sequence have to be cleaned before in order to conserve the alignment.

[adeena_hassan]

Hi.

I'm using ka ks calculator for ka ks ratio. But I'm too confused either it is working for multiple sequence alignment or only for a pair of sequences?

[romain.lannes]

Sorry for the delay, I actually didn't touch kaks for long. You may find here relevant information. Otherwise don't hesitate to ask a new question.