Dear Aidan, > I'm trying to figure out what the appropriate table for calculating > the CAIs of fission yeast sequences. > > The documentation says, "The default codon usage table 'Eyeastcai.cut' > was prepared from a set of S. pombe genes by Peter Rice." If you copy > the example in the documentation (that uses a fission yeast gene with > the Eyeastcai.cut table), you get the same results that they show.
Oops. Confusion (missing line) in the documentation for the cai application. We have tables for Saccharomyces cerevisiae and Schizosaccharomyces pombe. Fission yeast is in Eschpo_cai.cut, cerevisiae is in Eyeast_cai.cut. I will fix the docuemntation. In previous releases of EMBOSS the names were Epombecai.cut and Eyeastcai.cut. Release 4.0.0 has both names - future versions will use the new names to make the species clearer. I prepared both tables. Eyeast_cai.cut gives the published cerevisiae CAI values (the tables do not quite match the current gene sequences). Eschpo_cai.cut uses the same genes from S. pombe and is the one to use for fission yeast. The tabel was set uip for the pombe sequencers at Sanger. They may be able to give you more information about how useful the results are. Hope that helps, Peter _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
