TY - JOUR
T1 - The 'weighted sum of relative entropy'
T2 - A new index for synonymous codon usage bias
AU - Suzuki, Haruo
AU - Saito, Rintaro
AU - Tomita, Masaru
N1 - Funding Information:
We would like to thank Barry Zeeberg, Kunihiro Baba, and Hiromi Komai for their helpful interactions, and Kazuharu Arakawa for his technical advice on G-language GAE. This work was supported by the New Energy and Industrial Technology Development and Organization (NEDO) of the Ministry of Economy, Trade, and Industry of Japan (Development of a Technological Infrastructure for the Industrial Bioprocess Project), and the Ministry of Education, Culture, Sports, Science, and Technology, Grant-in-Aid for the 21st Century Center of Excellence (COE) Program entitled “Understanding and Control of Life's via Systems Biology (Keio University)”.
PY - 2004/6/23
Y1 - 2004/6/23
N2 - 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.
AB - 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.
KW - Amino acid usage bias
KW - E
KW - Gene expression level
KW - H
KW - H
KW - Nucleotide composition bias
KW - Shannon entropy
KW - Synonymous codon usage bias
KW - n
KW - the simple sum of entropy
KW - the weighted sum of entropy
KW - the weighted sum of relative entropy
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U2 - 10.1016/j.gene.2004.03.001
DO - 10.1016/j.gene.2004.03.001
M3 - Article
C2 - 15194186
AN - SCOPUS:2942582578
SN - 0378-1119
VL - 335
SP - 19
EP - 23
JO - Gene
JF - Gene
IS - 1-2
ER -