EMBOSS: codcmp

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)

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)

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

Output file format

This is the result of the example run:


# CODCMP codon usage table comparison
# Eeco.cut vs Ehin.cut

Sum Difference Squared = 2.337
Sum Difference         = 0.040
Codons not appearing   = 0

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

References

Warnings

Diagnostic Error Messages

Exit status

This program always exits with a status of 0.

Known bugs

Program name	Description
chaos	Create a chaos game representation plot for a sequence
chips	Codon usage statistics
compseq	Counts the composition of dimer/trimer/etc words in a sequence
cusp	Create a codon usage table
freak	Residue/base frequency table or plot
geecee	Calculates the fractional GC content of nucleic acid sequences
isochore	Plots isochores in large DNA sequences
newcpgreport	Report CpG rich areas
newcpgseek	Reports CpG rich regions
wobble	Wobble base plot
wordcount	Counts words of a specified size in a DNA sequence

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Completed 9 Sept 1999

Target users

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