:: DESCRIPTION
ENCprime is a program that calculates a codon usage bias summary statistic, Nc’. It is based on the effective number of codons statistic Nc (or ENC) developed by Frank Wright, but improves upon it by accounting for background nucleotide composition.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
CodonLogo is a tool for visualization of conserved codon patterns in multiple sequence alignments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Jul 15;28(14):1935-6. doi: 10.1093/bioinformatics/bts295. Epub 2012 May 17.
CodonLogo: a sequence logo-based viewer for codon patterns.
Sharma V1, Murphy DP, Provan G, Baranov PV.
:: DESCRIPTION
Sherlocc is a PERL written program able to scan Pfam protein families for conserved regions that have a low codon usage frequency (rare codon clusters). This program represents a novel approach as it is efficient enough to perform large-scale analysis of the proteome via the Pfam protein family database (representing about 70% of the known protein universe).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Jun 1;28(11):1438-45. doi: 10.1093/bioinformatics/bts149. Epub 2012 Mar 30.
Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events.
Chartier M, Gaudreault F, Najmanovich R.
:: DESCRIPTION
RCA (Relative codon adaptation) is a novel index for measuring codon adaptation in genomic sequences. Similar to CAI, RCA can use a reference geneset to estimate gene expression, but RCA takes directly into account the background nucleotide distribution.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
DNA Res. 2010 Jun;17(3):185-96. doi: 10.1093/dnares/dsq012. Epub 2010 May 7.
Relative codon adaptation: a generic codon bias index for prediction of gene expression.
Fox JM, Erill I.
:: DESCRIPTION
phyloExpCM is a Python package to implement experimentally determined codom models of substitution for phylogenetics.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bloom JD.
An experimentally determined evolutionary model dramatically improves phylogenetic fit.
Mol Biol Evol. 2014;31:1956-1978.
:: DESCRIPTION
GeneDesign is a codon manipulation library. Its main purpose is to ease the design and assembly of synthetic DNA.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Design-A-Gene with GeneDesign.
Richardson SM, Liu S, Boeke JD, Bader JS.
Methods Mol Biol. 2012;852:235-47. doi: 10.1007/978-1-61779-564-0_18.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
Genetic Code is a small app to translate nucleotide codons. Includes a small overview over the most common amino acids and nucleotides.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: DESCRIPTION
RescueNet (Relative Synonymous Codon Usage Neural Network) uses the Self-Organizing Map neural network algorithm for codon usage anaysis and gene-prediction. In its gene prediction functionality, RescueNet can estimate multiple models of gene codon usage properties during training. This offers advantageous gene-finding performance in cases where a diverse number of codon usage patterns are displayed. Examples include metagenomic datasets and prokaryotic genomes where mutational pressure, translational efficiency and horizontal gene transfer have diversified the displayed codon usage patterns.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.
Mahony S, McInerney JO, Smith TJ, Golden A.
BMC Bioinformatics. 2004 Mar 5;5:23.
