Abstract
The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure. We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of >17 000 times compared with single-core CPU, and >2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible. GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/m...Continue Reading
References
Dec 8, 2005·Applied and Environmental Microbiology·Catherine Lozupone, Rob Knight
Jul 6, 2006·Applied and Environmental Microbiology·T Z DeSantisG L Andersen
Mar 16, 2007·PLoS Biology·Rekha SeshadriMarvin Frazier
Dec 7, 2007·CBE Life Sciences Education·Anne JurkowskiJay B Labov
Feb 12, 2008·Trends in Genetics : TIG·Elaine R Mardis
Sep 23, 2008·BMC Bioinformatics·F MeyerR A Edwards
Aug 28, 2009·The ISME Journal·Micah HamadyRob Knight
Oct 6, 2009·Applied and Environmental Microbiology·Patrick D SchlossCarolyn F Weber
Feb 5, 2010·Bioinformatics·Donovan H Parks, Robert G Beiko
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Aug 28, 2010·Bioinformatics·Johannes GollShibu Yooseph
Jun 1, 2011·Genome Biology·J Gregory CaporasoRob Knight
Jun 22, 2011·Genome Research·Daniel H HusonStephan C Schuster
Oct 22, 2011·Bioinformatics·Tse-Yi WangHuai-Kuang Tsai
Jul 31, 2012·Bioinformatics·Xiaoquan SuKang Ning
Oct 12, 2012·BMC Systems Biology·Xiaoquan SuKang Ning
Citations
Sep 18, 2014·Scientific Reports·Xiaoquan SuKang Ning
Feb 8, 2020·Briefings in Bioinformatics·Mo ZhuKang Ning
Nov 10, 2018·Microbiome·Chen MaHeping Zhang
Nov 15, 2018·MBio·Xiaoquan SuJian Xu
Aug 8, 2019·MBio·Xiaoquan SuJian Xu
Dec 4, 2019·Bioinformatics·Gongchao JingXiaoquan Su
Mar 19, 2020·MSystems·Xiaoquan SuJian Xu
Aug 18, 2020·Computational and Structural Biotechnology Journal·Xiaoquan SuShunyao Wu
Jan 21, 2021·MSystems·Gongchao JingXiaoquan Su
Jul 14, 2021·MSystems·Gongchao JingJian Xu
Aug 18, 2021·MSystems·Xiaoquan Su