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Codon degeneracy and amino acid abundance influence the measures of codon usage bias: improved Nc ( N̂ c ) and ENCprime ( N̂ ′ c ) measures
Author(s) -
Satapathy Siddhartha Sankar,
Sahoo Ajit Kumar,
Ray Suvendra Kumar,
Ghosh Tapash Chandra
Publication year - 2017
Publication title -
genes to cells
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.912
H-Index - 115
eISSN - 1365-2443
pISSN - 1356-9597
DOI - 10.1111/gtc.12474
Subject(s) - codon usage bias , degeneracy (biology) , biology , amino acid , synonymous substitution , gene , genetics , genome
Effective number of codons (N^c) and its variant N^'c (effective number of codons prime) are the two widely used methods for measuring unequal usage of synonymous codons in coding sequences, known as the codon usage bias (CUB). The mathematical formula used in calculating N^c and N^'c values is giving inappropriate measures of CUB in case of low abundance of amino acids. In addition, the magnitude of error also varies according to codon degeneracy. In this study, a modified formula for N^c and N^'c 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.