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© Oxford University Press

Detection of genes in Escherichia coli sequences determined by genome projects and prediction of protein production levels, based on multivariate diversity in codon usage

Shigehiko Kanaya 1,*, Yoshihiro Kudo 1, Yasukazu Nakamura 2 and Toshimichi Ikemura 2

1Department of Electric and Information Engineering, Faculty of Engineering, Yamagata University Yonezawa, Yamagata-ken 992, Japan
2Department of Evolutionary Genetics, National Institute of Genetics, and the Graduate University for Advanced Studies Mishima, Shizuoka-ken 411, Japan

* To whom correspondence should be addressed. E-mail:kanaya{at}eie.yz.yamagata-u.ac.jp

We used principal component analysis to develop measures (called Z-parameters in this study) which reflect the diversity of codon usage in Escherichia coli genes. Protein production levels for 1500 CDSs (protein-coding sequences) identified by E.coli genome projects in Japan and the US were estimated from a correlation equation between Z1 and cellular protein content obtained through analysis of the genes experimentally characterized. Through the profile analysis of Z1 for E.coli sequences obtained by the Japanese Project, we predicted an additional 36 CDSs that had not been annotated in the International DNA Database. Thirty-one out of the 36 CDSs could be assigned to presumptive protein genes through a BLASTX search for recent protein databases in the Genome Net in Japan. Detailed examination of the Z1-parameter profile led us to assess sequencing errors which cause frame-shift.

Received on February 2, 1996; accepted on May 13, 1996

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