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The Journal of Supercomputing

, Volume 75, Issue 3, pp 1496–1509 | Cite as

Visualization of DNA methylation results through a GPU-based parallelization of the wavelet transform

  • Lisardo Fernández
  • Mariano Pérez
  • Juan M. OrduñaEmail author
Article
  • 75 Downloads

Abstract

Different statistical approaches have been proposed last years for finding differentially methylated DNA regions, starting from the outputs of DNA methylation analysis tools. However, these approaches do not allow an interactive and flexible exploration of these regions. Additionally, they add a high computation workload when used with large datasets. In this paper, we propose a new approach consisting in the transformation of DNA methylation results into a methylation signal and the Haar wavelet transformation of that signal for the displaying of the methylation results at different scales. Additionally, we propose the parallelization of the Haar wavelet transform on the GPU, as well as the GPU-based visualization of the methylation signal. The performance evaluation results show that this is the first proposal which allows the interactive visualization of different methylation signals with different resolution levels, in such a way that it can be used to visually detect differentially methylated regions accurately, in a user-friendly and flexible way, and with a very low computational workload.

Keywords

DNA methylation analysis Wavelet transform GPU computing GPU visualization 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Departamento de InformáticaUniversidad de ValenciaValenciaSpain

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