scNCA is a Java program to obtain the self-consistent reference set for a given genome using the NCA (or CAI) codon bias index. The self-consistent reference set is defined as the set of genes within the genome that possess a dominant codon bias, in the sense that ranking all genes in the genome with a codon usage index based on such a set leads to picking out the same set as the top-scoring group of genes in the genome. When translational bias is present, the self-consistent reference set is likely to be populated by genes with heavy translational bias, although other biases, such as %GC content, can confound the algorithm.
- Windows / MacOsX / Linux
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Carbone A, Zinovyev A, Képès F. (2003)
Codon adaptation index as a measure of dominating codon bias.
Bioinformatics, 19(16), 2005-15.