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Bioinformation. 2009 Sep 5;4(2):63-5.

On finding poorly translated codons based on their usage frequency.

Author information

  • 1Computational Biology Service Unit, Cornell University, Ithaca, NY 14853, USA. lp257@cornell.edu

Abstract

Long stretches of "rare" codons are known to severely inhibit the efficiency of translation. Understanding the distribution of such rare codons is of critical importance in improving the efficiency of heterologous gene expression systems. Accurate estimates of codon usage take the abundance of each protein into consideration. In this paper, we analyze the correlation between approximate measures of codon usage and the availability of tRNA at various growth rates in E coli. We show that the computationally derived estimates of tRNA isoacceptor concentration enable the finding of poorly translated codons.

KEYWORDS:

E coli; codon usage; codons; frequency; tRNA

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