CodonO – Analysis of Synonymous Codon Usage Bias

CodonO

:: DESCRIPTION

CodonO is a new informatics method for measuring synonymous codon usage bias within and across genomes. CodonO measures Synonymous Codon Usage Order (SCUO) in a genomic scale by connecting directly GenBank genomic database. CodonO plots SCUO and GC compositions.

::DEVELOPER

Systems Biology Laboratory, College of Veterinary Medicine,Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows

:: DOWNLOAD

CodonO

:: MORE INFORMATION

Citation

Wan, X.-F., J. Zhou, and D. Xu. 2006.
CodonO: a new informatics method measuring synonymous codon usage bias.
International Journal of General Systems, 35: 109-125.

CAIcal 1.4 – Assess Codon Usage Adaptation

CAIcal 1.4

:: DESCRIPTION

The CAIcal (Codon Adaptation Index calulator) server performs several computations in relation to codon usage and the codon adaptation of DNA or RNA sequences to host organisms.

::DEVELOPER

P. Puigbo, Ph.D.

:: SCREENSHOTS

:: REQUIREMENTS

Linux
Perl
TCL/TK

:: DOWNLOAD

CAIcal

:: MORE INFORMATION

Citation

Puigbo P, Bravo IG and Garcia-Vallve S. (2008)
CAIcal: a combined set of tools to assess codon usage adaptation.
Biology Direct, 3:38.

INCA 2.1 – INteractive Codon usage Analysis

INCA 2.1

:: DESCRIPTION

INCA provides an array of features useful in analysis of synonymous codon usage in whole genomes. In addition to computing codon frequencies and several usage indices, such as ‘codon bias’, effective Nc and CAI, the primary strength of INCA has numerous options for the interactive graphical display of calculated values, thus allowing visual detection of various trends in codon usage. Finally, INCA includes a specific unsupervised neural network algorithm, the self-organizing map, used for gene clustering according to the preferred utilization of codons.

::DEVELOPER

The Bioinformatics group

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

INCA

:: MORE INFORMATION

Citation:

Supek F, Vlahovicek K;
INCA: synonymous codon usage analysis and clustering by means of self-organizing map.
Bioinformatics. 2004 Sep 22;20(14):2329-2330

CodonW 1.4.4 – Codon Usage Analysis

CodonW 1.4.4

:: DESCRIPTION

CodonW is a package for codon usage analysis. It was designed to simplify Multivariate Analysis (MVA) of codon usage. The MVA method employed in CodonW is correspondence analysis (COA) (the most popular MVA method for codon usage analysis). CodonW can generate a COA for codon usage, relative synonymous codon usage or amino acid usage. Additional analyses of codon usage include investigation of optimal codons, codon and dinucleotide bias, and/or base composition. CodonW analyses sequences encoded by genetic codes other than the universal code.

::DEVELOPER

John Peden

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CodonW

:: MORE INFORMATION

Citation

Peden J.F.
Analysis of codon usage. 1999.
PhD Thesis, University of Nottingham, UK.