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RESEARCH PRODUCT
On the Use of Binary Trees for DNA Hydroxymethylation Analysis
Ana-bárbara GarcíaMariano PérezJuan M. OrduñaCésar GonzálezJavier Chavessubject
0301 basic medicineDNA Hydroxymethylation020203 distributed computingBinary treebusiness.industryComputer science02 engineering and technologyMethylationComputational biologySupercomputer03 medical and health scienceschemistry.chemical_compound030104 developmental biologySoftwareParallel softwarechemistryDNA methylation0202 electrical engineering electronic engineering information engineeringheterocyclic compoundsbusinessDNAdescription
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.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2017-01-01 |