title: Codon degeneracy and amino acid abundance influence the measures of codon usage bias: improved Nc (N̂c) and ENCprime (N̂'c) measures.
abstract: 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.
authors.affiliation: Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, 784028, Assam, India.
authors.forename: Siddhartha Sankar
authors.initials: SS
authors.lastname: Satapathy
authors.affiliation: Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur, 784028, Assam, India.
authors.forename: Ajit Kumar
authors.initials: AK
authors.lastname: Sahoo
authors.affiliation: Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur, 784028, Assam, India.
authors.forename: Suvendra Kumar
authors.initials: SK
authors.lastname: Ray
authors.affiliation: Bioinformatics Centre, Bose Institute, P-1/12, C.I.T. Scheme VII M, Kolkata, 700054, India.
authors.forename: Tapash Chandra
authors.initials: TC
authors.lastname: Ghosh
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics; D003062:Codon; D008957:Models, Genetic; D016366:Open Reading Frames; D012984:Software
chemical_list: D001426:Bacterial Proteins; D003062:Codon