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

Haruo Suzuki, Rintaro Saito, Masaru Tomita

研究成果: Article査読

20 被引用数 (Scopus)

抄録

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.

本文言語English
ページ(範囲)19-23
ページ数5
ジャーナルGene
335
1-2
DOI
出版ステータスPublished - 2004 6月 23

ASJC Scopus subject areas

  • 遺伝学

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