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Enhanced effective codon numbers to understand codon usage bias.

Authors
  • Smith, Reginald D1
  • 1 Ronin Institute 127 Haddon Pl, Montclair, NJ 07043, United States; Supreme Vinegar LLC, 3430 Progress Dr. Suite D, Bensalem, PA 19020, United States. Electronic address: [email protected] , (United States)
Type
Published Article
Journal
Bio Systems
Publication Date
Jul 13, 2022
Pages
104734–104734
Identifiers
DOI: 10.1016/j.biosystems.2022.104734
PMID: 35842072
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Codon usage bias is a well recognized phenomenon but the relative influence of its major causes: G+C content, mutational biases, and selection, are often difficult to disentangle. This paper presents methods to calculate modified effective codon numbers that allow the investigation of the sources of codon bias and how genes or organisms have their codon biases shaped. In particular, it demonstrates that variation in codon usage bias across organisms is likely driven more by likely mutational forces while the variation in codon usage bias within genomes is likely driven by codon selectional forces. Copyright © 2022 Elsevier B.V. All rights reserved.

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