GCUA -- General Codon Usage Analysis

GCUA is designed to calculate various parameters that might be relevant in assessing the codon usage patterns of a group of genes. The goal of this program was to provide an easy-to-use method (for free) of analysing codon usage in complete prokaryotic genomes. The user can look at codon usage (or any other statistic) in the dataset as a whole or for each gene individually. Variation in codon usage can be examined either by looking at distances between the genes based on their codon usage, or using multivariate analysis techniques (the user should get to know a little of the philosophies/methods of multivariate analyses before attempting this).

Features

The most relevant features of this program include:

• A Clustal-like menu interface
• Reads FASTA-formatted files
• Multivariate analyses of codon usage (RSCU) and amino acid patterns (Principle components, sum of squares and cross products, correspondence analysis, correlation analysis)
• Calculation of codon usage frequency
• Calculation of RSCU values
• Calculation of amino acid frequency data
• Calculation of base composition (GC1, GC2, GC3, GC3s)
• Calculation of distances between genes, based on RSCU values (PAUP and PHYLIP-compatible)
• Output in spreadsheet-readable format (Cricket Graph or MS Excel)
• Online help available
• Can be used in conjunction with the ADE package
• Universal and Mycoplasma/Spiroplasma code supported
• Ability to analyse complete prokaryotic genomes (up to 5,000 genes each with a maximum length of 15,000 bp)

Availability

The program is available by anonymous ftp in either tarred/compressed format for SUNOS or in stuffit/binhex format for PowerMAC.

Information provided by: James McInerney

Resources and further information

• The National History Museum
  http://www.nhm.ac.uk/
• The GCUA software
  ftp://ftp.nhm.ac.uk/pub/gcua/

External sites are not endorsed by EMBL-EBI

Direct questions or comments to Bioinformer Editor. This page last modified Friday, 16 July, 1999.
ISSN 1462-1363. More information about the BioInformer.

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