Codon degeneracy and amino acid abundance influence the measures of codon usage bias: improved Nc (N ̂c) and ENCprime (N̂′c) measures

In this study, a modified formula for and has been developed to measure the CUB more accurately. Online implementations of the modified formula are available in the web portal at http://agnigarh.tezu.ernet.in/~ssankar/cub.php.

Effective number of codons () and it's variant (Effective number of codons prime) are the two widely used methods for measuring codon usage bias (CUB) in coding sequences. The mathematical formula used in calculating and values are giving inappropriate measures of CUB in case of low abundance of amino acids and the magnitude of error varies according to codon degeneracy. In this study modified formula for and have been developed to measure the CUB more accurately whose online implementations are available in the web portal at http://agnigarh.tezu.ernet.in/~ssankar/cub.php.

Source: Genes to Cells - January 31, 2017 Category: Genetics & Stem Cells Authors: Siddhartha Sankar Satapathy, Ajit Kumar Sahoo, Suvendra Kumar Ray, Tapash Chandra Ghosh Tags: Original Article Source Type: research