| ## EMBOSS: chips

# Program chips

## Function

Codon usage statistics

## Description

chips calculates Frank Wright's Nc statistic for the effective number of codons used (ref 1).

This is a simple measure that quantifies how far the codon usage of a gene departs from equal usage of synonymous codons. This measure of synonymous codon usage bias, the 'effective number of codons used in a gene', Nc, can be easily calculated from codon usage data alone, and is independent of gene length and amino acid (aa) composition. Nc can take values from 20, in the case of extreme bias where one codon is exclusively used for each aa, to 61 when the use of alternative synonymous codons is equally likely. Nc thus provides an intuitively meaningful measure of the extent of codon preference in a gene.

The Nc statistic has problems in very short sequences (20 amino acids or less) which are yet to be fully resolved. They are caused by the need to consider amino acids which are missing in the sequence.

This calculation was originally in the EGCG package as "codfish" (codon usage for fission yeast). As Frank Wright is a vegan, we looked for a meat-free name for the EMBOSS version, "chips". The official explanation is "Codon Heterozygosity (Inverse of) in a Protein-coding Sequence"

## Usage

Here is a sample session with chips. If the sequence extends beyond the coding region then the start and/or end positions of the CDS must be provided because chips analyses exclusively protein coding regions.

    % chips -sbeg 135 -send 1292
    Input sequence: embl:paamir
    Output file [paamir.chips]:

## Command line arguments

       Mandatory qualifiers:
      [-seqall]            seqall     Sequence database USA
      [-outfile]           outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers:
       -cfile              codon      Codon usage file
       -window             integer    Averaging window

       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
--- | --- | ---
[-seqall] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.chips
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-cfile | Codon usage file | Codon usage file in EMBOSS data path | Ehum.cut
-window | Averaging window | Any integer value | 30

## Input file format

A nucleic acid sequence USA.

## Output file format

This is the output from the example run:

    # CHIPS codon usage statistics

    Nc = 32.951

If all codons are used, the Nc value will be 61. If only one codon is used for each amino acid the Nc value will be 20. Low values therefor indicate a strong codon bias, and high values indicate a low bias and possibly a non-coding region.

## Data files

chips reads a codon usage file but only as a template and ignores the original data.

The codon usage table is by default the file "CODONS/Ehum.cut" in the EMBOSS distribution directory.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by EMBOSS environment variable EMBOSS_DATA.

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## Notes

None.

## References

1. Wright, F. (1990) Gene 87:23-29 "The 'effective number of codons' used in a gene."

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
cai | CAI codon adaptation index
codcmp | Codon usage table comparison
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)

## History

1999 - Written - Alan Bleasby.

## Target users

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

## Comments