Parallel genomic sequence-search on a massively parallel system

2007 Computing Frontiers, Conference Proceedings

Volumn , Issue , 2007, Pages 59-68

  Thorsen, Oystein ^a   Smith, Brian ^a   Sosa, Carlos P ^b   Jiang, Karl ^a   Lin, Heshan ^c   Peters, Amanda ^a   Feng, Wu Chun ^d  

^a IBM   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c North Carolina State University   (United States)

^d State University   (United States)

Author keywords

Blue Gene L; Massively parallel computer; mpiBLAST PIO; Multiple masters parallelization

Indexed keywords

ALGORITHMS; COMPUTATIONAL COMPLEXITY; DATABASE SYSTEMS; RESOURCE ALLOCATION;

EFFICIENT FRAGMENT DISTRIBUTION; MULTIPLE MASTERS PARALLELIZATION; VIRTUAL FILE MANAGER;

PARALLEL PROCESSING SYSTEMS;

EID: 35348928208     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1242531.1242542     Document Type: Conference Paper

References (24)

1. Altschul, S., Gish, W., Miller, M., Myers, E., and Lipman, D. J. "Basic Local alignment Search Tool," Journal of Molecular Biology, vol. 215, pp. 403-410, 1990.
2. Galperin, M. Y. "The Molecular Biology Database Collection: Update," Nucleic Acids Research, vol. 34, pp. D3-D5, 2006.
3. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Wheeler, D. L. "GenBank," Nucleic Acids Research, vol. 34, pp. D16-D20, 2006.
4. Huai-hsin Chi, E., Shoop, E., Carlis, J., Retzel, E., and Riedl, J. "Efficiency of Shared-Memory Multiprocessors for a Genetic Sequence Similarity Search Algorithm," 1997. http://www-users.cs.umn.edu/~echi/ papers/perf/perf.html.
5. Altschul, S., Madden, T. L., Schaffer, A. A., Zheng, J., Zhang, Z., Miller, M., Lipman, D. J. "Gapped BLAST and PSI-BLAST. A New Generation of Protein Database Search Programs," Nucleic Acid Research, vol. 25, pp. 3389-3402, 1997.
6. th IEEE International Symposium on High Performance Distributed Computing, pp. 229-240, 2006.
7. Gardner, M. K., Feng, W. -C., Archuleta, J., Lin, H, Ma, X., "Parallel Genomic Sequence-Searching on an Ad-Hoc Grid: Experiences, Lessons Learned, and Implications," Supercomputing 2006, Florida.
8. Jiang, K., Thorse, O, Peters, A., Smith, B., and Sosa, C. P., "An Efficient Parallel Implementation of the Hidden Markov Methods on a Massively Parallel System," IEEE Transactions on Parallel and Distributed Systems 2007, accepted.
9. Sosa, CP., Accapadi, M., and Atyam, B. V. "BLAST Throughput Benchmarks: mmap versus read," in Performance Marketing Council 2003, Ed. Stahl, E., REDP-3692-00, IBM Corporation, International Technical Support Organization, Austin, TX, 2003. http://publibb.boulder.ibm. com/Redbooks.nsf/RedpaperAbstracts/redp3692.html?Open
10. Sosa, C. P., Tu, Z. J., and Fast, P. L. "Some Practical Suggestions for Performing NCBI BLAST Benchmarks on a pSeries 690 System," REDP-043 7-00, IBM Corporation, International Technical Support Organization Austin, TX, 2002. http://www.redbooks.ibm.com/abstracts/redp0437.html?Open
11. Lascu, O., Allsopp, N., Vezolle, P., Follows, J., Hennecke, M., Ishibashi, F., Paolini, M., Prakash, S., Reddy, H., Sosa, C P., Tabary, A., Quintero, D. "Unfolding the IBM Server Blue Gene Solution," SG24-6686-00, IBM Corporation, International Technical Support Organization, Poughkeepsie, NY, 2005, http://www.redbooks.ibm.com/abstracts/ sg246686.html?Open
12. Braun, R. C., Pedretti, K. T., Casavart, T. L., Sheetz, T. E., Birkett, C L., and Roberts, C A. "Parallelization of Local BLAST Service on Workstation Clusters," Future Generation Computer Systems, vol. 17, pp. 745-754, 2001.
13. th International Conference on Linux Clusters in conjunction with ClusterWorld, 2003.
14. th International Parallel and Distributed Processing Symp. (IPDPS), 2005.
15. Message Passing Interface Forum. MPI: Message-Passing Interface Standard, June 1995.
16. Nieplocha, J., Harrison, R., and Littlefield, R. "Global Arrays: A Nonuniform Memory Access Programming Model for High-Performance Computing," J. Supercomputing vol. 10, pp. 197-220, 1996.
17. Oehmen, C and J. Nieplocha, "ScalaBLAST: A Scalable Implementation of BLAST for High-Performance DataIntensive Bioinformatics Analysis," IEEE Transactions on Parallel and Distributed Systems, vol. 17, pp. 740-749, 2006.
18. Meng, X. and Chaudhary, V. "Bio-Sequence Analysis with Cradle's 3SoCTM Software Scalable System on Chip," Proc. ACMSymp. Applied Computing, 2004.
19. th IEEE International Workshop on High-Performance Computational Biology, 2005.
20. th International Parallel and Distributed Processing Symp. (IPDPS), 2002.
21. Camp, N., Cofer, H., and Gomperts, R., "High-Throughput BLAST," 1998.
22. Bachega, L.; Lantz, E., Moore, N, Rangwala, H., "Life Science Application Analysis Speed Team," Final Report, IBM, Rochester, MN, September 2005.
23. Rangwala, H., Lantz, E., Musselman, R., Pinnow, K., Smith, B., and Wallenfelt, B. "Massively Parallel BLAST for the Blue Gene/L," High Availability and Performance Workshop, 2005. http://xcr.cenit.latech.edu/ hapcw2005/papers/final_bglBLAST.pdf.
24. Standard set of BLAST databases for Nucleotide, Protein, and Translated BLAST searches are made available at: ftp://ftp.ncbi.nih.gov/blast/db/ in pre-formatted format. The FASTA databases reside under the /blast/db/FASTA directory.