[Biopython] codon bias

[Peter Cock]

On Tue, Oct 29, 2013 at 1:05 PM, Jessica Grant <jgrant at smith.edu> wrote:
> Hello again,
>
> I am resending to clarify - I am wondering if anyone has
> implemented  Wright's Effective Number of Codons (as in Wright, F. 1990.
> The effective number of codons used in a gene. Gene 87:23-29), or any
> improved method.  I have tried using codonW but got some wonky results.  I
> am working with transcriptome data from a non-model organism and want to
> look at the relationships between ENc, GC3 and other statistics to tease
> out any information about the data in my transcriptome.
>
> Thanks,
>
> Jessica
>
> On Fri, Oct 25, 2013 at 1:44 PM, Jessica Grant <jgrant at smith.edu> wrote:
>
>> Hello,
>>
>> I was wondering if anyone had some code to determine effective number of
>> codons in a sequence.  I'm working with an organism with a non-canonical
>> genetic code, so I don't think I can use any of the standard packages.
>>
>> Thanks,
>>
>> Jessica
>>

I emailed Frank (we both work at the James Hutton Institute, although
he is under the BioSS organisation):
http://www.hutton.ac.uk/staff/frank-wright
http://www.bioss.ac.uk/people/frank.html

Frank suggests looking at the EMBOSS implementation 'chips',
http://emboss.sourceforge.net/apps/release/6.5/emboss/apps/chips.html

Peter