Exploiting multi-grain parallelism for efficient selective sweep detection

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7439 LNCS, Issue PART 1, 2012, Pages 56-68

  Alachiotis, Nikolaos ^a   Pavlidis, Pavlos ^a   Stamatakis, Alexandros ^a  

^a HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EXECUTION TIME; FINE GRAIN PARALLELISM; LOAD IMBALANCE; MOLECULAR DATA; MULTI-GRAIN; MULTIPLE SEQUENCE ALIGNMENTS; NUMBER OF THREADS; OPEN SOURCE TOOLS; PARALLEL EFFICIENCY; PARALLEL VERSION; PARALLELIZATIONS; PERFORMANCE ASSESSMENT; PERFORMANCE ISSUES; POPULATION GENETICS; POSITIVE SELECTION; RUNTIMES; SELECTIVE SWEEP; SIMULATED DATASETS; SINGLE NUCLEOTIDE POLYMORPHISMS;

ALGORITHMS;

POPULATION STATISTICS;

EID: 84866654437     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-33078-0_5     Document Type: Conference Paper

References (11)

1. Maynard Smith, J., Haigh, J.: The hitch-hiking effect of a favourable gene. Genet. Res. 23(1), 23-35 (1974)
2. Kim, Y., Nielsen, R.: Linkage disequilibrium as a signature of selective sweeps. Genetics 167(3), 1513-1524 (2004)
3. Jensen, J.D., Thornton, K.R., Bustamante, C.D., Aquadro, C.F.: On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. Genetics 176(4), 2371-2379 (2007)
4. Pavlidis, P., Jensen, J.D., Stephan,W.: Searching for footprints of positive selection in whole-genome snp data from nonequilibrium populations. Genetics 185(3), 907-922 (2010)
5. Berger, S.A., Stamatakis, A.: Assessment of barrier implementations for fine-grain parallel regions on current multi-core architectures. In: Proc. IEEE Int Cluster Computing Workshops and Posters (CLUSTER WORKSHOPS) Conf., pp. 1-8 (2010)
6. Stamatakis, A., Komornik, Z., Berger, S.A.: Evolutionary placement of short sequence reads on multi-core architectures. In: Proceedings of the ACS/IEEE International Conference on Computer Systems and Applications (AICCSA 2010), pp. 1-8. IEEE Computer Society Press, Washington (2010)
7. Blagojevic, F., Nikolopoulos, D.S., Stamatakis, A., Antonopoulos, C.D.: Dynamic multigrain parallelization on the cell broadband engine. In: Proceedings of the 12th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP 2007, pp. 90-100. ACM, New York (2007)
8. Kimura, M.: The number of heterozygous nucleotide sites maintained in a nite population due to steady ux of mutations. Genetics 61(4), 893-903 (1969)
9. Hudson, R.R.: Generating samples under a wright-fisher neutral model of genetic variation. Bioinformatics 18(2), 337-338 (2002)
10. Gillespie, J.H.: Population genetics: a concise guide. Johns Hopkins Univ. Pr. (2004)
11. Haddrill, P.R., Thornton, K.R., Charlesworth, B., Andolfatto, P.: Multilocus patterns of nucleotide variability and the demographic and selection history of drosophila melanogaster populations. Genome Res. 15(6), 790-799 (2005)