Emboss-cusp

Predict codon usage tables from nucleotide sequences using the EMBOSS cusp tool.

Annotation languageWebsite scheduleApril 3, 2026

Installation

Create a conda environment to install EMBOSS

conda create -n Emboss_env

Install EMBOSS on this environment

conda install -n Emboss_env -c bioconda emboss

Run

cusp input_file.fna output_file

The only thing you need to run is a nucleotide sequence. The output file generated will be saved with the extension .cusp.

Output

This is an example of the beginning of an output:

#CdsCount: 1

#Coding GC 67.79%
#1st letter GC 67.88%
#2nd letter GC 46.89%
#3rd letter GC 88.60%

#Codon AA Fraction Frequency Number
GCA    A     0.077     7.772      3
GCC    A     0.462    46.632     18
GCG    A     0.462    46.632     18

GC usage

The first valuable information is the GC usage in codons. This can be correlated with the GC content of the genome.

In the main table we can see the other information:

Column	Description
Codon	Sequence of the codon.
AA	The encoded amino acid.
Fraction	The proportion of usage of the codon among its redundant set, i.e. the set of codons which code for this codon's amino acid.
Frequency	The expected number of codons, given the input sequence(s), per 1000 bases. This will be an extrapolation if the sequence is shorter than 1000 bases.
Number	The observed number of codons in the input sequences.