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Identification of DNA CpG Islands Using Inter-dinucleotide Distances

  • Vera AfreixoEmail author
  • Carlos A. C. Bastos
  • João M. O. S. Rodrigues
  • Raquel M. Silva
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 499)

Abstract

In this study we set to explore the potentialities of the inter-genomic symbols distance for finding CpG islands in DNA sequences. We explore the distance distributions of the inter CpG and SS distance in the independent nucleotide context (reference). We confront the empirical results from the complete human genome, CpG islands and non CpG islands, with the corresponding reference results.

We propose a model to discriminate CpG islands based on some statistical properties of the inter-dinucleotide distances distributions in DNA sequences. The results of this exploratory study suggest that inter-SS symbols distance has high ability to discriminate CpG islands.

Keywords

State Diagram Distance Distribution Reference Distribution Symbol Distance Absorb Markov Chain 
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 International Publishing Switzerland 2015

Authors and Affiliations

  • Vera Afreixo
    • 1
    • 2
    • 4
    Email author
  • Carlos A. C. Bastos
    • 2
    • 3
  • João M. O. S. Rodrigues
    • 2
    • 3
  • Raquel M. Silva
    • 1
    • 2
  1. 1.CIDMA - Center for Research and Development in Mathematics and ApplicationsUniversity of AveiroAveiroPortugal
  2. 2.IEETA - Institute of Electronics and Telematics Engineering of AveiroUniversity of AveiroAveiroPortugal
  3. 3.Department of Electronics Telecommunications and InformaticsUniversity of AveiroAveiroPortugal
  4. 4.Institute for Research in Biomedicine - iBiMEDUniversity of AveiroAveiroPortugal

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