title: P-Hint-Hunt: a deep parallelized whole genome DNA methylation detection tool.
abstract: The increasing studies have been conducted using whole genome DNA methylation detection as one of the most important part of epigenetics research to find the significant relationships among DNA methylation and several typical diseases, such as cancers and diabetes. In many of those studies, mapping the bisulfite treated sequence to the whole genome has been the main method to study DNA cytosine methylation. However, today's relative tools almost suffer from inaccuracies and time-consuming problems.
  
  
  
  In our study, we designed a new DNA methylation prediction tool ("Hint-Hunt") to solve the problem. By having an optimal complex alignment computation and Smith-Waterman matrix dynamic programming, Hint-Hunt could analyze and predict the DNA methylation status. But when Hint-Hunt tried to predict DNA methylation status with large-scale dataset, there are still slow speed and low temporal-spatial efficiency problems. In order to solve the problems of Smith-Waterman dynamic programming and low temporal-spatial efficiency, we further design a deep parallelized whole genome DNA methylation detection tool ("P-Hint-Hunt") on Tianhe-2 (TH-2) supercomputer.
  
  
  
  To the best of our knowledge, P-Hint-Hunt is the first parallel DNA methylation detection tool with a high speed-up to process large-scale dataset, and could run both on CPU and Intel Xeon Phi coprocessors. Moreover, we deploy and evaluate Hint-Hunt and P-Hint-Hunt on TH-2 supercomputer in different scales. The experimental results illuminate our tools eliminate the deviation caused by bisulfite treatment in mapping procedure and the multi-level parallel program yields a 48 times speed-up with 64 threads. P-Hint-Hunt gain a deep acceleration on CPU and Intel Xeon Phi heterogeneous platform, which gives full play of the advantages of multi-cores (CPU) and many-cores (Phi).
authors.affiliation: School of Computer Science, National University of Defense Technology, Changsha, China. pengshaoliang@nudt.edu.cn.
authors.forename: Shaoliang
authors.initials: S
authors.lastname: Peng
authors.affiliation: School of Computer Science, National University of Defense Technology, Changsha, China.
authors.forename: Shunyun
authors.initials: S
authors.lastname: Yang
authors.affiliation: School of Computer Science, National University of Defense Technology, Changsha, China. gaoming@nudt.edu.cn.
authors.forename: Ming
authors.initials: M
authors.lastname: Gao
authors.affiliation: School of Computer Science, National University of Defense Technology, Changsha, China.
authors.forename: Xiangke
authors.initials: X
authors.lastname: Liao
authors.affiliation: School of Computer Science, National University of Defense Technology, Changsha, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
authors.affiliation: School of Computer Science, National University of Defense Technology, Changsha, China.
authors.forename: Canqun
authors.initials: C
authors.lastname: Yang
authors.affiliation: Faculty of Life Sciences, University of Manchester, Manchester, UK.
authors.forename: Chengkun
authors.initials: C
authors.lastname: Wu
authors.affiliation: EpiRNA Lab, Institues of Biomedical Sciences, Fudan University, Shanghai, China.
authors.forename: Wenqiang
authors.initials: W
authors.lastname: Yu
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003596:Cytosine / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D015894:Genome, Human; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D003596:Cytosine
keywords: DNA methylation detection; Parallelized algorithm; Tianhe-2; Whole genome; Xeon Phi