[EMBOSS] EMBOSS cai

[pmr at ebi.ac.uk]

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