The methylation of DNA is 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.
Journal: IEEE/ACM transactions on computational biology and bioinformatics