Using markov chains of nucleotide sequences as a possible precursor to predict functional roles of human genome: A case study on inactive chromatin regions

K. E. Lee, E. J. Lee, H. S. Park

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Abstract

Recent advances in computational epigenetics have provided new opportunities to evaluate n-gram probabilistic language models. In this paper, we describe a systematic genome-wide approach for predicting functional roles in inactive chromatin regions by using a sequence-based Markovian chromatin map of the human genome. We demonstrate that Markov chains of sequences can be used as a precursor to predict functional roles in heterochromatin regions and provide an example comparing two publicly available chromatin annotations of large-scale epigenomics projects: ENCODE project consortium and Roadmap Epigenomics consortium.

Original languageEnglish
Article number15039004
JournalGenetics and Molecular Research
Volume15
Issue number3
DOIs
StatePublished - 30 Aug 2016

Bibliographical note

Publisher Copyright:
© 2016 The Authors.

Keywords

  • Chromatin maps
  • Computational epigenetics
  • Markov chain
  • Noncoding DNA
  • Nucleotide frequency patterns

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