[Biopython] codon bias

[Jessica Grant]

I have chips up and running!  Thanks so much!


On Wed, Oct 30, 2013 at 7:15 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> 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
>