Tag: Reference Set

scNCA – Obtain Self-consistent Reference Set using NCA (or CAI) Codon Bias Index

scNCA

:: DESCRIPTION

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.

::DEVELOPER

the Erill Lab

:: SCREENSHOTS

scNCA

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

scNCA

:: MORE INFORMATION

Citation

Carbone A, Zinovyev A, Képès F. (2003)
Codon adaptation index as a measure of dominating codon bias.
Bioinformatics, 19(16), 2005-15.