Accelerating multiple sequence alignment with the Cell BE processor

Computer Journal

Volumn 53, Issue 6, 2010, Pages 814-826

  Vandierendonck, Hans ^a   Rul, Sean ^a   De Bosschere, Koen ^a  

^a GHENT UNIVERSITY   (Belgium)

Author keywords

Bio informatics; Cell broadband engine; Parallelization

Indexed keywords

CELL BROADBAND ENGINE; GENERAL PURPOSE PROCESSORS; HETEROGENEOUS MULTICORE; MULTIPLE SEQUENCE ALIGNMENTS; OPTIMIZED IMPLEMENTATION; PARALLELIZATIONS; POWER PROCESSING UNITS; SYNERGISTIC PROCESSORS;

CELLS; CYTOLOGY; ENGINES; GENERAL PURPOSE COMPUTERS; INFORMATION SCIENCE; MICROPROCESSOR CHIPS;

COMPUTER ARCHITECTURE;

EID: 80052539337     PISSN: 00104620     EISSN: 14602067     Source Type: Journal    
DOI: 10.1093/comjnl/bxp086     Document Type: Article

References (22)

1. Pham, D. et al. (2005) The Design and Implementation of a First-Generation Cell Processor. IEEE Int. Solid-State Circuits Conf., San Francisco, CA, January 6-10, pp. 184-592. IEEE Computer Society, Los Alamitos, CA, USA.
2. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
3. Flachs, B. et al. (2006) The microarchitecture of the synergistic processor for a Cell processor. IEEE J. Solid-State Circuits, 41, 63-70.
4. Gschwind, M., Hofstee, PH., Flachs, B., Hopkins, M., Watanabe, Y. and Yamazaki, T. (2006) Synergistic processing in cell's multicore architecture. IEEE Micro., 26, 10-24.
5. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
6. Just, W. (2001) Computational complexity of multiple sequence alignment with SP-score. J. Comput. Biol, 8, 615-623.
7. Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol, 4, 406-425.
8. Vandierendonck, H, Rul, S., Questier, M. and De Bosschere, K. (2008) Experiences with Parallelizing a Bio-informatics Program on the Cell BE. 3rd HiPEAC Conf., Göteborg, Sweden, January 27-29, pp. 161-175. Springer, Berlin, Heidelberg.
9. Chaichoompu, K., Kittitornkun, S. and Tongsima, S. (2006) MT-ClustalW: Multithreading Multiple Sequence Alignment. Fifth IEEE Int. Workshop on High Performance Computational Biology, Rhodes Island, Greece, April 25, p. 8. IEEE Computer Society, Los Alamitos, CA, USA.
10. Liu, Y., Schmidt, B. and Maskell, D.L. (2009) MSA-CUDA: Multiple SequenceAlignmenton Graphics Processing Units with CUDA. Proc. ICCS 2009, Part I, Lecture Notes in Computer Science 5544, Baton Rouge, LO, May 25-27, pp. 962-971.
11. Horowitz, E. and Sahni, S. (1987) Data Structures in Pascal. Computer Science Press.
12. Bader, D., Li, Y., Li, T. and Sachdeva, V. (2005) BioPerf: A Benchmark Suite to Evaluate High-Performance Computer Architecture on Bioinformatics Applications. The IEEE Int. Symp. Workload Characterization, Austin, TX, October 6-8, pp. 163-173. IEEE Computer Society, Los Alamitos, CA, USA.
13. Williams, S., Shalf, J., Oliker, L., Kamil, S., Husbands, P. and Yelick, K. (2006) The Potential of the Cell Processor for Scientific Computing. Proc. 3rd Conf. Computing Frontiers, Ischia, Italy, May 2-5, pp. 9-20. ACM.
14. Barker, K.J., Davis, K., Hoisie, A., Kerbyson, D. J., Lang, M., Pakin, S. and Sancho, J. C. (2008) Entering the petaflop era: the architecture and performance of Roadrunner. In SC '08: Proc. 2008 ACM/IEEE conference on Supercomputing, Austin, Texas, pp. 1-11. IEEE Press, Piscataway, NJ.
15. Greene, J. and Cooper, R. (2006). A Parallel 64K Complex FFT Algorithm for the IBM/Sony/Toshiba Cell Broadband Engine Processor. Mercury Computer Systems, Chelmsford, MA.
16. Heman, S., Nes, N., Zukowski, M. and Boncz, P.A. (2007) Vectorized Data Processing on the Cell Broadband Engine. Proc. Int. Workshop on Data Management on New Hardware, Beijing, China, June 15, pp. 1-6. ACM Press, New York, NY, USA.
17. Bader, D.A., Agarwal, V. and Madduri, K. (2007) On the Design and Analysis of Irregular Algorithms on the Cell Processor: A Case Study on List Ranking. 21st IEEE Int. Parallel and Distributed Processing Symp., Long Beach, CA, March 26-30, pp. 76-85. IEEE Computer Society, Los Alamitos, CA, USA.
18. Blagojevic, F., Stamatakis, A., Antonopoulos, C.D. and Nikolopoulos, D.E. (2007) RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine. Int. Symp. Parallel and Distributed Processing Systems, Long Beach, CA, March 26-30, pp. 1-10. IEEE Computer Society, Los Alamitos, CA, USA.
19. Sachdeva, V., Kistler, M., Speight, E. and Tzeng, T.-H.K. (2008) Exploring the Viability of the Cell Broadband Engine for Bioinformatics Applications. Parallel Comput., 34, 616-626.
20. Liu, W., Schmidt, B., Voss, G. and Muller-Wittig, W. (2007) Streaming algorithms for biological sequence alignment on GPUs. IEEE Trans. Parallel Distrib. Syst., 18, 1270-1281.
21. Farrar, M. (2007) Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinfor-matics, 23, 156-161.
22. Sarje, A. and Aluru, S. (2009) Parallel genomic alignments on the Cell Broadband Engine. IEEE Trans. Parallel Distrib. Syst., 20, to appear.