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On the Use of Binary Trees for DNA Hydroxymethylation Analysis

  • César González
  • Mariano Pérez
  • Juan M. OrduñaEmail author
  • Javier Chaves
  • Ana-Bárbara García
Conference paper
  • 1.8k Downloads
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10393)

Abstract

DNA methylation (mC) and hydroxymethylation (hmC) can have a significant effect on normal human development, health and disease status. Hydroxymethylation studies require specific treatment of DNA, as well as software tools for their analysis. In this paper, we propose a parallel software tool for analyzing the DNA hydroxymethylation data obtained by TAB-seq. The software is based on the use of binary trees for searching the different occurrences of methylation and hydroxymethylation in DNA samples. The binary trees allow to efficiently store and access the information about the methylation of each methylated/hydroxymethylated cytosines in the samples. Evaluation results shows that the performance of the application is only limited by the computer input/output bandwidth, even for the case of very long samples.

Keywords

High performance computing DNA hydroxymethylation Parallel pipeline 

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • César González
    • 1
  • Mariano Pérez
    • 1
  • Juan M. Orduña
    • 1
    Email author
  • Javier Chaves
    • 2
  • Ana-Bárbara García
    • 2
  1. 1.Depto. de InformáticaUniversidad de ValenciaBurjassot, ValenciaSpain
  2. 2.INCLIVA Health Research Institute, CIBERDEM (Carlos III Health Institute)ValenciaSpain

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