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codcmp |
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.
This compares the codon usage tables for Escherichia coli and Haemophilus influenzae.
% codcmp Codon usage table comparison Codon usage file [Ehum.cut]: Eeco.cut Codon usage file [Ehum.cut]: Ehin.cut Output file [outfile.codcmp]: |
Go to the output files for this example
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) Associated qualifiers: "-outfile" related qualifiers -odirectory3 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for required and optional values -debug boolean Write debug output to program.dbg -acdlog boolean Write ACD processing log to program.acdlog -acdpretty boolean Rewrite ACD file as program.acdpretty -acdtable boolean Write HTML table of options -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths |
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) |
# 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 |
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
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 |
Some more statistics were added by
David Martin (dmartin © hgmp.mrc.ac.uk)