密码子简并性和氨基酸丰度影响密码子使用偏好的度量：改进的 Nc（N̂）和 ENCprime（N̂）度量。

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

机构信息

Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, 784028, Assam, India.

Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur, 784028, Assam, India.

出版信息

Genes Cells. 2017 Mar;22(3):277-283. doi: 10.1111/gtc.12474. Epub 2017 Feb 10.

DOI:10.1111/gtc.12474

PMID:28185367

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.

摘要

有效密码子数 (N^c) 及其变体 N^'c（有效密码子基数）是两种广泛用于衡量编码序列中同义密码子使用不均等的方法，即密码子使用偏性（CUB）。在计算 N^c 和 N^'c 值时使用的数学公式在氨基酸丰度低的情况下给出了 CUB 的不适当度量。此外，误差的大小也根据密码子简并性而变化。在这项研究中，开发了一种改进的 N^c 和 N^'c 公式，以更准确地衡量 CUB。该改进公式的在线实现可在 http://agnigarh.tezu.ernet.in/~ssankar/cub.php 的网络门户中获得。