Journal article
Validation of computational prediction of horizontal gene transfer events—XenoCluster
The Journal of Supercomputing, Vol.57(2), pp.141-150
08/2011
DOI: 10.1007/s11227-010-0386-2
Abstract
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).
Details
- Title: Subtitle
- Validation of computational prediction of horizontal gene transfer events—XenoCluster
- Creators
- Jesse Walters - Department of Electrical and Computer Engineering University of Iowa Iowa City IA 52242 USAThomas Bair - Coordinated Laboratory for Computational Genomics University of Iowa Iowa City IA 52242 USATerry Braun - Department of Ophthalmology and Visual Sciences University of Iowa Iowa City IA 52242 USATodd Scheetz - Department of Ophthalmology and Visual Sciences University of Iowa Iowa City IA 52242 USAJohn Robinson - Center for Bioinformatics and Computational Biology University of Iowa Iowa City IA 52242 USAThomas Casavant - Department of Biomedical Engineering University of Iowa Iowa City IA 52242 USA
- Contributors
- Victor Malyshkin (Editor)
- Resource Type
- Journal article
- Publication Details
- The Journal of Supercomputing, Vol.57(2), pp.141-150
- Publisher
- Springer US; Boston
- DOI
- 10.1007/s11227-010-0386-2
- ISSN
- 0920-8542
- eISSN
- 1573-0484
- Language
- English
- Date published
- 08/2011
- Academic Unit
- Ophthalmology and Visual Sciences; Electrical and Computer Engineering; Roy J. Carver Department of Biomedical Engineering
- Record Identifier
- 9983979935302771
Metrics
18 Record Views