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P-Hint-Hunt: a deep parallelized whole genome DNA methylation detection tool

Overview of attention for article published in BMC Genomics, March 2017
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Title
P-Hint-Hunt: a deep parallelized whole genome DNA methylation detection tool
Published in
BMC Genomics, March 2017
DOI 10.1186/s12864-017-3497-9
Pubmed ID
Authors

Shaoliang Peng, Shunyun Yang, Ming Gao, Xiangke Liao, Jie Liu, Canqun Yang, Chengkun Wu, Wenqiang Yu

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).

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 8 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 8 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 2 25%
Other 1 13%
Student > Bachelor 1 13%
Student > Doctoral Student 1 13%
Student > Master 1 13%
Other 1 13%
Unknown 1 13%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 1 13%
Mathematics 1 13%
Nursing and Health Professions 1 13%
Agricultural and Biological Sciences 1 13%
Computer Science 1 13%
Other 2 25%
Unknown 1 13%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 May 2017.
All research outputs
#14,338,684
of 24,093,053 outputs
Outputs from BMC Genomics
#5,233
of 10,906 outputs
Outputs of similar age
#163,337
of 311,394 outputs
Outputs of similar age from BMC Genomics
#92
of 199 outputs
Altmetric has tracked 24,093,053 research outputs across all sources so far. This one is in the 39th percentile – i.e., 39% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,906 research outputs from this source. They receive a mean Attention Score of 4.8. This one is in the 49th percentile – i.e., 49% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 311,394 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 45th percentile – i.e., 45% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 199 others from the same source and published within six weeks on either side of this one. This one is in the 49th percentile – i.e., 49% of its contemporaries scored the same or lower than it.