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RESEARCH PRODUCT
HPG-HMapper: A DNA hydroxymethylation analysis tool
César GonzálezAna-bárbara GarcíaMariano PérezJuan M. OrduñaJavier Chavessubject
DNA Hydroxymethylation0303 health sciencesDisease statusComputer scienceParallel pipelineComputational biologyTheoretical Computer Science03 medical and health scienceschemistry.chemical_compound0302 clinical medicinechemistryHardware and ArchitectureDNA methylationA-DNA030217 neurology & neurosurgerySoftwareDNA030304 developmental biologydescription
DNA methylation (mC) and hydroxymethylation (hmC) can significantly affect the normal human development, as well as health and disease status. hmC studies require not only specific treatment of DNA, but also software tools for their analysis. However, there are no software tools capable of analyzing DNA hmC currently. In this article, we propose HPG-HMapper, a parallel software tool for analyzing the DNA hmC data obtained by ten-eleven translocation–assisted bisulfite sequencing. This tool takes as input data the output files of mC aligner tools, and it yields mC maps and the accounting of methylated and hydroxymethylated bases on each chromosome. The design of this tool includes the consideration of different approaches, one of them based on binary trees and the other one based on bit arrays. The performance evaluation results show that a hybrid implementation is the most efficient option, allowing fast read and update operations while keeping a small memory footprint.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2019-04-15 | The International Journal of High Performance Computing Applications |