KaKs calculator

Question

[Abdukhalim Khon]

Hi everyone. I am working with eremurus species. This is my first individual work and I have 27 new sequenced chloroplast genomes of Eremurus. I want calculate Ka/Ks values between these species. I have read lots of articles like this and most of them used similar method to do it like this:

"A total of 53 coding sequences (CDSs) (>300 bp) in the plastid genome of Chamaesium were used to analyze the ratios of the synonymous site (Ks) and non-synonymous site (Ka). These 53 CDSs were aligned with MAFFT v. 7 [65]. Manual alterations were performed by MEGA6 [67]. Pairwise Ka/Ks ratios of the nine species were calculated based on the 53 CDS alignments in KaKs Calculator 2.0"

I have aligned 27 eremurus species with MAFFT in Geneious, then extracted all CDS from the alignment. Overall, 80 CDS have been extracte. All CDS have been aligned on MegaX. But when I use Ka/Ks calculator 2.0, the results appearinh for only the genes. I can't getting results between species. I mean I want Ka/Ks values between 27 species with each other. How can I do that?

Is anyone can help me? Please!!!

If there is video tutorials for this, attach it also. Please!!!

[Elaine Wang]

Hi, you could check a software names KaKs Calculator (DOI: 10.1016/S1672-0229(07)60007-2) not KaKs Calculator 2.0 probably, i am using it now but haven't got the result yet, hope it would be helpful.

Btw have you solved your question, i am also getting stuck by similar stuff. I would also like to get the KaKs ratio of 150 CDS sequences from 120 species, just spotted your question when i google it, may i ask how did you analyse it finally if it has been worked out?

Many thanks!

Answer 1

[lieven.sterck]

To some extent this is expected behaviour, Ks/Kn can only be computed between two sequences.

If you want to get estimates on a per species basis you can do, and what most will do in this case. is to concatenate your CDS sequences into one big "virtual" CDS and use those for alignment and Ks/Kn calculation.

Caution: keep very well track of the individual elements as well such to for instance they all algin on the respective counterpart CDS of another species.

For more info, search on "phylogeny with concatenate alignments"

[Abdukhalim Khon]

In order to do the that, I should align one chloroplast sequence of Eremurus with another with MAFFT on Geneious software, then extract all CDS one by one, export as a fasta sequence, then I sholud convert that fasta files to .axt format and calculate Ka/Ks ratio on Ka/Ks calculator. Then I sholud do these jobs with the other 26 Eremurus species. Is it right? I think I am wrong. Can you help me to do it right, please!

[lieven.sterck]

I don't really know that specific tool (Ka/ks calculator) so I can't advice you there.

What I would do (and often did) is this: you extract/select the CDS sequences of each species. You concatenate them per species , in the same order obviously, then align that large virtual sequence en calculate the Ks/Kn . Those estimates are always pairwise so you will have to calculate that for all possible pairs.