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

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

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

.........

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

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

Program name	Description
backtranseq	Back translate a protein sequence
chaos	Create a chaos game representation plot for a sequence
chips	Codon usage statistics
codcmp	Codon usage table comparison
compseq	Counts the composition of dimer/trimer/etc words in a sequence
freak	Residue/base frequency table or plot
geecee	Calculates the fractional GC content of nucleic acid sequences
getorf	Finds and extracts open reading frames (ORFs)
isochore	Plots isochores in large DNA sequences
newcpgreport	Report CpG rich areas
newcpgseek	Reports CpG rich regions
plotorf	Plot potential open reading frames
prettyseq	Output sequence with translated ranges
remap	Display a sequence with restriction cut sites, translation etc
showorf	Pretty output of DNA translations
showseq	Display a sequence with features, translation etc
syco	Synonymous codon usage Gribskov statistic plot
transeq	Translate nucleic acid sequences
wobble	Wobble base plot
wordcount	Counts words of a specified size in a DNA sequence

Author(s)

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

History

Target users

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