The 'weighted sum of relative entropy': A new index for synonymous codon usage bias

Haruo Suzuki, Rintaro Saito, Masaru Tomita

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Shannon entropy from information theory has been applied to estimate the degree of deviation from equal usage of synonymous codons; however, previous attempts have failed to take into account all three aspects of amino acid usage, i.e. (i) the number of distinct amino acids, (ii) their relative frequencies, and (iii) their degree of codon degeneracy. A new index taking into account all of these aspects is proposed. The index, designated as the 'weighted sum of relative entropy' (Ew), is defined as the sum of the relative entropy of each amino acid weighted by its relative frequency in the sequence. In this paper, we demonstrate that Ew allows us to avoid some amino acid usage biases and can yield results contradictory to those obtained by previous methods.

Original languageEnglish
Pages (from-to)19-23
Number of pages5
JournalGene
Volume335
Issue number1-2
DOIs
Publication statusPublished - 2004 Jun 23

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Entropy
Codon
Amino Acids
Information Theory

Keywords

  • Amino acid usage bias
  • E
  • Gene expression level
  • H
  • H
  • n
  • Nucleotide composition bias
  • Shannon entropy
  • Synonymous codon usage bias
  • the simple sum of entropy
  • the weighted sum of entropy
  • the weighted sum of relative entropy

ASJC Scopus subject areas

  • Genetics

Cite this

The 'weighted sum of relative entropy' : A new index for synonymous codon usage bias. / Suzuki, Haruo; Saito, Rintaro; Tomita, Masaru.

In: Gene, Vol. 335, No. 1-2, 23.06.2004, p. 19-23.

Research output: Contribution to journalArticle

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