Conservative vs non-conservative substitutions

[Claudia Weber]

The PLoS One paper describing the applications for substitution mapping mentions that it would be possible to pool amino acid substitutions into conservative vs non-conservative substitutions. Is this currently implemented? I can't find any reference to it in the manual, but it would be interesting to look at.

Thanks,
Claudia

[Julien Yann Dutheil]

Dear Claudia,

This is not implemented yet, but the framework is there to do so,
providing we would have a definition of what is conservative and what
is not, as it can depend on your protein of interest. Maybe the
easiest would be to read it from a file, in a format similar to PAML
substitution models, which would define the different categories of
substitutions to count. Would that fit your needs?

All the best,

Julien.

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--
Julien Y. Dutheil, Ph-D
0 (+49) 6421 178 530

§ Max Planck Institute for Terrestrial Microbiology
Department of Organismic Interactions
Marburg -- GERMANY

§ Intitute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE

[Claudia Weber]

Dear Julien,

Thanks for the quick response! Yes, I think that a flexible solution similar to the mtCDNA example in PAML where OmegaAA.dat specifies different classes of substitution would be quite useful. Given how fast substitution mapping is, this would also make it easy to compare several different definitions where appropriate.

Claudia