| ## EMBOSS: cusp

# Program cusp

## Function

Create a codon usage table

## Description

Reads one or more coding sequences (CDS sequence only) and calculates a codon frequency table.

The output file can be used as a codon usage table in other applications.

## Usage

Here is a sample session with cusp, using just one sequence. Normal use would be to extract a set of coding sequences and to use these as input.

    % cusp -sbeg 135 -send 1292
    Create a codon usage table
    Input sequence: embl:paamir
    Output file [paamir.cusp]:

## Command line arguments

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

       Optional qualifiers: (none)
       Advanced qualifiers:
       -cfile              codon      Codon usage table name

       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
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.cusp
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-cfile | Codon usage table name | Codon usage file in EMBOSS data path | Ehum.cut

## Input file format

## Output file format

Here is the start of the output from the example run, which used a single CDS from Pseudomonas aeruginosa which has a very high GC content ands a strong coding bias, as shown by the codons for Alanine where those ending with G or C are used almost exclusively.

    # CUSP codon usage file
    # Codon Amino acid      Fract   /1000   Number
    GCA     A               0.077   7.772   3
    GCC     A               0.462   46.632  18
    GCG     A               0.462   46.632  18
    GCT     A               0.000   0.000   0

    .........

The 'Fract' column gives the faction of all amino acids coded for by this codon triplet.

The /1000 column represents the number of codons, given the input sequence(s), there are per 1000 bases. This will be an extrapolation if the sequence is shorter than 1000 bases.

If multiple sequences are input then the statistics are given for all of the sequences together, not individually.

## Data files

cusp reads a codon usage file, but only as a template and does not use any of the data so any file will give the same results.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

Always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
cai | CAI codon adaptation index
chips | Codon usage statistics
codcmp | Codon usage table comparison
syco | Synonymous codon usage Gribskov statistic plot

## Author(s)

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

## History

Spring 2000 - written

## Target users

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

## Comments