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Classic Cryptanalysis Applied to Exons and Introns Prediction

  • Manuel Aguilar R.
  • Héctor Fraire H.
  • Laura Cruz R.
  • Juan J. González B.
  • Guadalupe Castilla V.
  • Claudia G. Gómez S.
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4707)

Abstract

Prediction of exonic and intronic regions is an important problem of bioinformatics, which has been solved with a set of medium accuracy coding measures. In this work, we propose a new methodology for the prediction of exons and introns based on a cryptanalysis method of Kasiski, using variants of three classical coding measures: codon usage, amino acid usage, and codon preference. We validated our approach testing a set of 178 sequence of different length, improving the prediction of exons level reported by Fickett. Additionally we introduce the first results of introns prediction with an accuracy level of 83.4%.

Keywords

Intronic Region Code Model Synonymous Codon Nucleic Acid Research Codon Preference 
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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References

  1. 1.
    Griffiths, A., Gelbart, W., Lewontin, R., Miller, J.: Modern Genetic Analysis, 2nd edn (2002)Google Scholar
  2. 2.
    Santos, A.: Criptoanalisis del Código Genético. Universidad de la Coruña. Tesis de Maestria (2000)Google Scholar
  3. 3.
    Staden, R.: Codon preference and its use in identifying protein coding regions in long dna sequences. Nucleic Acids Research (1982)Google Scholar
  4. 4.
    McCaldon, P., Argos, P.: Proteins: Structure, Function and Genetics 4, 99–122 (1988)Google Scholar
  5. 5.
    Fickett, J.W., Tung, C.S.: Assessment of protein coding measures. Nucleic Acids Research 20, 6441–6450 (1992)CrossRefGoogle Scholar
  6. 6.
    Gribskov, M., Devereux, J., Burgess, R.B.: The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression. Nucleic Acids Research 12, 539–549 (1984)CrossRefGoogle Scholar
  7. 7.
    Gebbie, S.: A survey of the Mathematics of Cryptology. Masther’s Thesis. University of the Witwatersrand, Johanesburg (2003)Google Scholar
  8. 8.
    Software Predictor de Genes, http://augustus.gobics.de/

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Manuel Aguilar R.
    • 1
  • Héctor Fraire H.
    • 1
  • Laura Cruz R.
    • 1
  • Juan J. González B.
    • 1
  • Guadalupe Castilla V.
    • 1
  • Claudia G. Gómez S.
    • 1
  1. 1.Instituto Tecnológico de Ciudad Madero 

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