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Mutually symmetric and complementary triplets: differences in their use distinguish systematically between coding and

Christoforos Nikolaou1, Yannis Almirantis

  • 1National Research Center for Physical Sciences Demokritos, Institute of Biology, 15310 Athens, Greece.

Journal of Theoretical Biology
|July 24, 2003
PubMed
Summary

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This study quantifies asymmetry in genomic sequences, revealing that reading frame differences predict protein-coding regions. This linguistic asymmetry in DNA reflects the genetic code and codon usage biases.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Meaningful texts exhibit word use asymmetry, a property observed across languages.
  • Genomic sequences possess inherent structural and functional asymmetries.

Purpose of the Study:

  • To quantify differences in triplet usage within genomic sequences to identify coding regions.
  • To explore the predictive power of sequence asymmetry for protein-coding identification.
  • To relate linguistic asymmetry in DNA to the genetic code and codon usage biases.

Main Methods:

  • Quantification of mutually symmetric triplet usage across three reading frames in genomic sequences.
  • Quantification of complementary triplet usage in genomic sequences.
  • Analysis of sequence asymmetry in relation to coding potential.

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Main Results:

  • High values of symmetric triplet asymmetry in a specific reading frame indicate a protein-coding sequence.
  • Complementary triplet asymmetry also predicts the coding character of a sequence.
  • Observed asymmetries reflect the non-equivalence between sense and anti-sense DNA strands.

Conclusions:

  • Linguistic asymmetry is a fundamental property of coding genomic sequences.
  • The genetic code structure and codon usage bias contribute to observed sequence asymmetries.
  • These methods provide insights into DNA sequence characteristics and coding potential.