Journal
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
Volume 17, Issue 1, Pages 220-225Publisher
IEEE COMPUTER SOC
DOI: 10.1109/TCBB.2018.2861399
Keywords
Genomics; Bioinformatics; DNA; Tools; Sequential analysis; Instruction sets; Pipelines; DNA methylation motifs; motif finding; multi threads; MultiMotifMaker; Pacbio reads
Categories
Funding
- National Natural Science Foundation of China [61772552, 61420106009, 61622213]
- 111 Project [B18059]
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The methylation of DNA is an important mechanism to control biological processes. Recently, the Pacbio SMRT technology provides a new way to identify base methylation in the genome. MotifMaker is a tool developed by Pacbio for discovering DNA methylation motifs from methylated DNA sequences. However, MotifMaker is single-threaded and computational expensive for identifying methylation motifs from large genomes. Here, we present an efficient motif finding algorithm (MultiMotifMaker) by implementing multi threads of the MotifMaker. The MultiMotifMaker speeds up the motif search about 8-9 times on a 32 core computer comparing to MotifMaker. MultiMotifMaker makes it possible to identify methylation motifs from Pacbio reads for large genomes.
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