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Title
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On finding poorly translated codons based on their usage frequency |
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Authors
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Lalit Ponnala | |
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Affiliation
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Computational Biology Service Unit, Cornell University, Ithaca NY 14853, USA | |
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Article Type
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Hypothesis | |
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Date
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Received June 16, 2009; Accepted July 18, 2009; Published September 05, 2009 | |
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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. | |
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Keywords
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codons; codon usage; tRNA; frequency; E. coli | |
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Citation
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Ponnala, Bioinformation 4(2): 63-65 (2009) | |
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Edited by
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P. Kangueane
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ISSN
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0973-2063
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Publisher
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License
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This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License. |