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Codon bias index in K. lactis

Peter Rice pmr at sanger.ac.uk
Fri Jul 31 09:01:04 EST 1998


"RNDr.Zeman Igor         150" <izeman at fns.uniba.sk> writes:
> I would like to compare CAI (Codon Adaptation Index) and/or CBI (codon
> bias index) of one gene from K. lactis with homologs in S. cerevisiae.
> I hope that somebody can help me with this task. There are some
> internet sites for calculations (I know only site for S. cerevisiae
> genes). I am not sure whether site for K. lactis genes (or other
> non-conventional yeast genes) exists. Some programs calculating these
> indexes in K. lactis have also been released. Any hint will be
> helpful.

I implemented something for Schizosaccharomyces pombe in the EGCG
package a while back - in a program called "codfish" after "codon usage"
and "fission yeast" :-).

I need to investigate this topic again for its successor (the EMBOSS
package), especially as we have yeast sequencers in house.

The problems that came up originally included reproducing CAI values
where the cerevisiae gene sequences had changed slightly since the
original calculations, and wondering how to handle CAI and CBI values
in other species. In cerevisiae, for example, both codons for Asp were
ignored by CBI and Ala codon GCC was ignored by CAI. It was unclear
what to do about other cases such as CTT and CTC in S.pombe which were
candidates for inclusion in CBI. At the time there was no defined set
of highly expressed S.pombe genes to base the table on so it used a
general S.pombe codon usage table.

There is a K.lactis codon usage table from the U. Otago TRANSTERM
database at:

ftp://ftp.ebi.ac.uk/pub/databases/transterm/kla.cod

-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/



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