CodonW a codon usage analysis program [AnnCodonW home page:ounce]

John Peden johnp at molbiol.ox.ac.uk
Wed Jul 16 12:51:03 EST 1997


CodonW home page:
http://www.molbiol.ox.ac.uk/cu

Binaries and Source code can be downloaded from
 ftp://molbiol.ox.ac.uk/cu or via the home page given above.

CodonW is a freeware program for codon usage analysis. It was designed
to simplify Multivariate Analysis (MVA) of codon usage. The MVA method
used is correspondence analysis (COA), the most popular MVA method used
for analysis of codon usage. CodonW can analyse codon usage, relative
synonymous codon usage and amino acid usage. 

CodonW measures other properties of codon usage (e.g. GC, GC3s, codon
base and dinucleotide composition, and Number of synonymous codons). It
calculates the following codon usage indices - Frequency of optimal
codons (Fop), Codon Adaptation Index (CAI), Effective Number of codons
(ENc) and Codon Bias Index (CBI); as well as the amino acid GRAVY and
Aromaticity scores. It tabulates codon and amino acid usage for
individual genes or the total dataset. CodonW was designed to work with
and calculate indices for all variations of the genetic code.  

CodonW was primarily designed to be driven via a series of nested
text-based menus (each with its own help).  There is also a
comprehensive commandline interface. Codonw also checks the name used to
invoke it, if this is one of a predetermined list (e.g. gc, enc, fop,
cai, cu ....  see README.links), it will emulate an appropriate codon
usage analysis program (bypassing both the menu and commandline
interface).

The vast majority of prokaryotic and eukaryotic species have non-random
codon usage. The major factor in codon choice in many unicellular and
some multicellular organisms is Darwinian selection between synonyms,
with highly expressed genes using a restricted set of codons. This
selection is almost certainly for optimal translational efficiency, and
is most pronounced in highly expressed genes in species whose effective
population size is large. CodonW was designed to investigate this
process, and automatically identifies those codons which appear to be
"optimal".

This is a beta release of the software so please email me if you install
the program; I can then keep you informed of any bugs/updates. Please
contact me with any problems or comments.


John

________________________________________________________________________
John Peden                    | johnP at molbiol.ox.ac.uk
Molecular Biology Data Centre |   
University of Oxford          |  
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