Journal Article

Conservation of Translation Initiation Sites Based on Dinucleotide Frequency and Codon Usage in <i>Escherichia coli</i> K-12 (W3110): Non-random Distribution of A/T-rich Sequences Immediately Upstream of the Translation Initiation Codon

Kazuo Yamagishi, Taku Oshima, Yasushi Masuda, Takeshi Ara, Shigehiko Kanaya and Hirotada Mori

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 9, issue 1, pages 19-24
Published in print January 2002 | ISSN: 1340-2838
Published online January 2002 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/9.1.19

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Dinucleotide frequencies are useful for characterizing consensus elements as a minimum unit of nucleotide sequence because the neighborhood relations of nucleotide sequences are reflected in dinucleotides. Using a consensus score based on dinucleotide frequencies and intra-species codon usage heterogeneity, denoted by the Z1 parameter, we report the relationship between nucleotide conservation at the translation initiation sites of genes in the Escherichia coli K-12 genome (W3110) and codon usage in its downstream genes. Significant positive correlations were obtained in three regions centered at −13, −4, and +7, which correspond to the Shine-Dalgarno element, the A + T element immediately upstream of the translation initiation site, and the downstream box, respectively.

Keywords: Escherichia coli K-12 (W3110); translation initiation; codon usage; dinucleotide

Journal Article.  0 words. 

Subjects: Genetics and Genomics

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