caa a22 4500 44585250X CHVBK 20180317145417.0 cr unu---uuuuu 170323e20110801xx s 000 0 eng 10.1007/s11227-010-0386-2 doi (NATIONALLICENCE)springer-10.1007/s11227-010-0386-2 Validation of computational prediction of horizontal gene transfer events—XenoCluster [Elektronische Daten] [Jesse Walters, Thomas Bair, Terry Braun, Todd Scheetz, John Robinson, Thomas Casavant] In this paper, we assess the biological accuracy and relevance of XenoCluster results compared to a reported set of known xenologs in yeast (Hall et al. Eukaryot. Cell 4(6):1102-1115, 2005). We were able to assign a high-priority rank to all reported yeast xenologs for which we had sufficient genomic sequence data. Additionally, we now report on a fine-grained extension to our previous implementation (Walters et al. 8th International Parallel Computing Technologies Conference (PaCT), LNCS, vol. 3606, pp. 355-366, Springer, Berlin, 2005), in which we achieved 80% efficiency on 8 CPU cores. In the coarse-grained component, high degrees parallelism (up to 65x speedup on 4,096 processors) was reported. While an obvious candidate for coarse-grained implementation, this paper now describes a multiple granularity parallelism solution that includes exploitation of multicore shared memory nodes to address fine-grained aspects in the tree-clustering phase of our previous deployment of XenoCluster (Walters et al. 8th International Parallel Computing Technologies Conference (PaCT), LNCS, vol. 3606, pp. 355-366, Springer, Berlin, 2005). Springer Science+Business Media, LLC, 2010 Multi-scale parallel computing nationallicence Genome annotation nationallicence DNA nationallicence Evolution nationallicence Walters Jesse Coordinated Laboratory for Computational Genomics, University of Iowa, 52242, Iowa City, IA, USA aut Bair Thomas Coordinated Laboratory for Computational Genomics, University of Iowa, 52242, Iowa City, IA, USA aut Braun Terry Coordinated Laboratory for Computational Genomics, University of Iowa, 52242, Iowa City, IA, USA aut Scheetz Todd Coordinated Laboratory for Computational Genomics, University of Iowa, 52242, Iowa City, IA, USA aut Robinson John Department of Electrical and Computer Engineering, University of Iowa, 52242, Iowa City, IA, USA aut Casavant Thomas Coordinated Laboratory for Computational Genomics, University of Iowa, 52242, Iowa City, IA, USA aut The Journal of Supercomputing Springer US; http://www.springer-ny.com 57/2(2011-08-01), 141-150 0920-8542 57:2<141 2011 57 11227 https://doi.org/10.1007/s11227-010-0386-2 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s11227-010-0386-2 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Walters Jesse Coordinated Laboratory for Computational Genomics, University of Iowa, 52242, Iowa City, IA, USA aut NATIONALLICENCE 700 1- Bair Thomas Coordinated Laboratory for Computational Genomics, University of Iowa, 52242, Iowa City, IA, USA aut NATIONALLICENCE 700 1- Braun Terry Coordinated Laboratory for Computational Genomics, University of Iowa, 52242, Iowa City, IA, USA aut NATIONALLICENCE 700 1- Scheetz Todd Coordinated Laboratory for Computational Genomics, University of Iowa, 52242, Iowa City, IA, USA aut NATIONALLICENCE 700 1- Robinson John Department of Electrical and Computer Engineering, University of Iowa, 52242, Iowa City, IA, USA aut NATIONALLICENCE 700 1- Casavant Thomas Coordinated Laboratory for Computational Genomics, University of Iowa, 52242, Iowa City, IA, USA aut NATIONALLICENCE 773 0- The Journal of Supercomputing Springer US; http://www.springer-ny.com 57/2(2011-08-01), 141-150 0920-8542 57:2<141 2011 57 11227 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer