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Measures of Codon Bias in Yeast, the tRNA Pairing Index and Possible DNA Repair Mechanisms

  • Markus T. Friberg
  • Pedro Gonnet
  • Yves Barral
  • Nicol N. Schraudolph
  • Gaston H. Gonnet
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4175)

Abstract

Protein translation is a rapid and accurate process, which has been optimized by evolution. Recently, it has been shown that tRNA reusage influences translation speed. We present the tRNA Pairing Index (TPI), a novel index to measure the degree of tRNA reusage in any gene. We describe two variants of the index, how to combine various such indices to a single one and an efficient algorithm for their computation. A statistical analysis of gene expression groups indicate that cell cycle genes have high TPI. This result is independent of other biases like GC content and codon bias. Furthermore, we find an additional unexpected codon bias that seems related to a context sensitive DNA repair.

Keywords

Codon Usage Synonymous Codon Codon Bias Individual Amino Acid Cell Cycle Gene 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Markus T. Friberg
    • 1
  • Pedro Gonnet
    • 1
  • Yves Barral
    • 2
  • Nicol N. Schraudolph
    • 3
    • 4
  • Gaston H. Gonnet
    • 1
  1. 1.Institute of Computational ScienceETH ZurichZurichSwitzerland
  2. 2.Institute of Biochemistry, Department of BiologyETH ZurichSwitzerland
  3. 3.Statistical Machine LearningNational ICT AustraliaCanberraAustralia
  4. 4.RSISEAustralian National UniversityCanberraAustralia

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