codon usage bias

James McInerney jamm at nhm.ac.uk
Wed Aug 27 07:03:42 EST 1997


Janssens at agr.kuleuven.ac.be wrote:
> 
> Hi,
> 
> I'm looking for a method to analyse differences in codon usage tables.
> I know
> the gcg programs codonfrequency, preference and correspond, but what
> I'm
> looking for is a way to calculate the error-level. I tried it with
> chi-square,
> but that seems not to be correct. Does anyone know a SAS-program to do
> this or
> another downloadable algorithm.
> 
> Thanks,
> 
> Hans Vermeiren
> FA Janssens Laboratory for Genetics
> W. De Croylaan 42
> B-3001 Heverlee
> janssens at agr.kuleuven.ac.be

Hans,


I have made a program available for analysing codon usage variation.  It is
available from:
 
ftp://ftp.nhm.ac.uk/pub/gcua.

It is designed to analyse differences in codon usage patterns.  It might do
what you wish.

Alternatively, you could try John Peden's program available from:

http://www.molbiol.ox.ac.uk/cu

which might also do what you wish.

Email me privately if you wish to elaborate on your request.

James

-- 
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James O. McInerney               email: J.mcinerney at nhm.ac.uk
Senior Scientific Officer,       phone: +44 171 938 9247
Department of Zoology,           Fax:   +44 171 938 9158
The Natural History Museum,
Cromwell Road,                    
London SW7 5BD.                  
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