cusp

Function

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

Command line arguments


Input file format

Output file format

The example usage read in 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.

The 'Fract' column gives that proportion of usage of a given codon among its redundant set (i.e. the set of codons which code for this codon's amino acid). For example, the sum of the 6 codons representing serine will add up to 1.00.

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 codon usage file from any species 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.

Author(s)

History

Target users

Comments