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Notes on application for codon usage / composition bias

 Subject: Re: [EMBOSS] Codon usage comparisons
From: "Thiago Venancio" 
Date: Tue, September 6, 2005 12:04 pm
To: "Jon Ison" 
Priority: Normal
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Dear Jon,

Thanks for your reply. I was studying this topic and
found some papers that
could help, specially the ENCprime, written by John
Novembre. In his
personel home page, he let the C code available for
download and the paper
references. His program compensate for nucleic acid
composition bias and is
less affected by sequence sizes.

There is also a paper published by Urrutia and Hurst in
2001. (Genetics 159:
1191-1199).

If you need some more tips, feel free to email me.

Cheers.

Thiago

On 9/6/05, Jon Ison  wrote:
>
> Dear Thiago
>
> So far as I'm aware there's no compensation made for
amino acid
> composition, but it would be a nice complement to
programs such
> as cai (http://emboss.sourceforge.net/apps/cai.html).
>
> If you could let us know the key papers and whether
any code
> exists we can consider incorporating such in the future.
>
> Cheers
>
> Jon
>
>
> > Hi all.
> > I have a couple questions about the codon usage
comparisons in the
> EMBOSS.
> > I have read some papers that use Factorial
Correspondence Analysis to
> > compensate for aminoacid composition. The EMBOSS
tools compensate it by
> > some
> > other way or what we get could be a biased result?
> >
> > Regards.
> >
> > Thiago
> >
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS@emboss.open-bio.org
> > http://newportal.open-bio.org/mailman/listinfo/emboss
> >
>
>
>


-- 
Thiago Motta Venancio
Bioinformatics PhD student

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