[EMBOSS] CUTG

[Peter Rice]

Carole Louis wrote:

> Thank you. I'm looking for Spodoptera frugiperda. I thought it was
> Espo.cut but it seems very different of the table I found at
> http://www.kazusa.or.jp/codon/. 

Spo.cut would be Schizosaccharomyces pombe.

After you run cutgextract on the cutg database from 
ftp.ebi.ac.uk/pub/databases/cutg you should have 
ESpodoptera_frugiperda.cut which comes from the gbinv.codons file.

The kazusa service looks interesting ... I wonder whether EMBOSS could 
read codon usage tables directly from there on request... I will try to 
make that work if there is enough interest.

>>----- Original Message ----- 
>>        From: Carole Louis
>>        To: Liste Emboss
>>        
>>        I extracted the CUTG database with cutgextract without any
>>        problem but I'd like to have a more explicite name for my .cut
>>        files ? Is it possible to obtain it ?

We are working on improving the naming and descriptions of codon usage 
files - for EMBOSS 2.9.0. This will have to include cutgextract output.

Does anyone need the codon usage files included in the EMBOSS 
distribution? We would like to "retire" the old ones (the long names) 
and rename (and update) the cutg ones.

regards,

Peter Rice