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

M. T. Friberg, P. Gonnet, Y. Barral, N. N. Schraudolph, and G. H. Gonnet. Measures of Codon Bias in Yeast, the tRNA Pairing Index and Possible DNA Repair Mechanisms. In Algorithms in Bioinformatics: 6th Intl. Workshop (WABI), pp. 1–11, Springer Verlag, Berlin, Zurich, Switzerland, 2006.

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Abstract

Protein translation is a rapid and accurate process, which has been optimized by evolution. Recently, it was shown that tRNA reusage influences translation speed. Here we present the TPI (tRNA Pairing Index), 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.

BibTeX Entry

@inproceedings{FriGonBarSchetal06,
     author = {Markus T. Friberg and Pedro Gonnet and Yves Barral and
               Nicol N. Schraudolph and Gaston H. Gonnet},
      title = {\href{http://nic.schraudolph.org/pubs/FriGonBarSchetal06.pdf}{
               Measures of Codon Bias in Yeast, the {tRNA} Pairing Index
               and Possible {DNA} Repair Mechanisms}},
      pages = {1--11},
     editor = {Philipp B\"ucher and Bernard M. E. Moret},
  booktitle = {Algorithms in Bioinformatics:
               6$^{th}$ Intl.\ Workshop (WABI)},
     volume =  4175,
     series = {Lecture Notes in Bioinformatics},
    address = {Zurich, Switzerland},
  publisher = {\href{http://www.springer.de/}{Springer Verlag}, Berlin},
       year =  2006,
   b2h_type = {Other},
  b2h_topic = {Bioinformatics},
   abstract = {
    Protein translation is a rapid and accurate process, which has
    been optimized by evolution. Recently, it was shown that tRNA
    reusage influences translation speed. Here we present the TPI
    (tRNA Pairing Index), 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.
}}

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