
                               EMBOSS: codcmp
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                                Program codcmp
                                       
Function

   Codon usage table comparison
   
Description

   This program reads in two codon usage table files.
   
   It counts the number of the 64 possible codons which are unused (i.e.
   has a usage fraction of 0) in either one or the other or both of the
   codon usage tables.
   
   The usage fraction of a codon is its proportion (0 to 1) of the total
   of the codons in the sequences used to construct the usage table.
   
   For each codon that is used in both tables, it takes the difference
   between the usage fraction. The sum of the differences and the sum of
   the differences squared is reported in the output file, together with
   the number of unused codons.
   
Usage

   Here is a sample session with codcmp, comparing the codon usage tables
   for Escherichia coli and Haemophilus influenzae.
   
% codcmp
Codon usage file [Ehum.cut]: Eeco.cut
Codon usage file [Ehum.cut]: Ehin.cut
Output file [outfile.codcmp]:

Command line arguments

   Mandatory qualifiers:
  [-first]             codon      First codon usage file
  [-second]            codon      Second codon usage file
  [-outfile]           outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-first]
   (Parameter 1) First codon usage file Codon usage file in EMBOSS data
   path Ehum.cut
   [-second]
   (Parameter 2) Second codon usage file Codon usage file in EMBOSS data
   path Ehum.cut
   [-outfile]
   (Parameter 3) Output file name Output file <sequence>.codcmp
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   It reads in the Codon Usage Tables - these are available as EMBOSS
   data files. See below for details.
   
Output file format

   This is the result of the example run:
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# CODCMP codon usage table comparison
# Eeco.cut vs Ehin.cut

Sum Squared Difference = 2.337
Mean Squared Difference = 0.037
Root Mean Squared Difference = 0.191
Sum Difference         = 9.840
Mean Difference         = 0.154
Codons not appearing   = 0
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Data files

   The codon usage tables are read by default from "Ehum.cut" in the
   data/CODONS directory of the EMBOSS distribution.
   
   If the name of a codon usage file is specified on the command line,
   then this file will first be searched for in the current directory and
   then in the 'data/CODONS' directory of the EMBOSS distribution.
   
   To see the available EMBOSS codon usage files, run:

% embossdata -showall

   To fetch one of the codon usage tables (for example 'Emus.cut') into
   your current directory for you to inspect or modify, run:

% embossdata -fetch -file Emus.cut

Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   This program always exits with a status of 0.
   
Known bugs

   None.
   
See also

   Program name                  Description
   cai          CAI codon adaptation index
   chips        Codon usage statistics
   cusp         Create a codon usage table
   syco         Synonymous codon usage Gribskov statistic plot
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
   Some more statistics were add by David Martin
   (david.martin@biotek.uio.no)
   
History

   Completed 9 Sept 1999
   20 Oct 2000 - David Martin added a couple more statistics to the
   output.
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
