Hi JP, No there isn't a class to calculate dN/dS. At a basic level dN/dS is a very easy ratio to calculate if you take the very basic approach of sequences of exact lengths. The basics of it are available from:
http://pubmlst.org/software/analysis/start/manual/dsdn.shtml The best package I know of to calculate the rates though is codeml. It's a very awkward program to run but it can be done & will produce the best results. I can say for sure that the Ensembl Compara team use it to calculate dN/dS rates for their homologous protein sets. Hope that helps, Andy P.S. I say all of this from personal experience when I wrote a very basic calculator using BioJava (and I don't know where the code got to). The amount of work to produce that code vs. running a third party application just makes it more cost effective to go for the 3rd party app JP wrote: > Hi there - is there a class or method which finds the dN/dS ratio > (nonsynonymous/synonymous rate ratio) for two sequences ? > > Many Thanks > JP > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
