Pairwise distance matrix computation for multiple sequence alignment on the cell broadband engine

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

Volumn 5544 LNCS, Issue PART 1, 2009, Pages 954-963

  Wirawan, Adrianto ^a   Schmidt, Bertil ^a   Kwoh, Chee Keong ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

Cell broadband engine; Multiple sequence alignment

Indexed keywords

ACCELERATOR TECHNOLOGY; BIOINFORMATICS APPLICATIONS; BIOLOGICAL DATA; CELL BROADBAND ENGINE; COMPUTATIONAL PLATFORMS; DISTANCE MATRICES; EXECUTION TIME; EXPONENTIAL GROWTH; MULTIPLE SEQUENCE ALIGNMENT; MULTIPLE SEQUENCE ALIGNMENT ALGORITHM; MULTIPLE SEQUENCE ALIGNMENTS; PAIRWISE DISTANCES; PLAYSTATION;

ALIGNMENT; BIOINFORMATICS; CELL MEMBRANES; MATRIX ALGEBRA;

HEURISTIC ALGORITHMS;

EID: 68849113648     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-01970-8_96     Document Type: Conference Paper

References (24)

1. Lipman, D.J., Altschul, S.F., Kececioglu, J.D.: A tool for multiple sequence alignment. Proceedings of the National Academy of Sciences of the United States of America 86(12), 4412-4415 (1989)
2. Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22(22), 4673-4680 (1994)
3. Notredame, C., Higgins, D.G., Heringa, J.: T-coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302(1), 205-217 (2000)
4. Katoh, K., Misawa, K., Kuma, K.I., Miyata, T.: MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30(14), 3059-3066 (2002)
5. Schmollinger, M., Nieselt, K., Kaufmann, M., Morgenstern, B.: DIALIGN P: Fast pairwise and multiple sequence alignment using parallel processors. BMC Bioinformatics, 5 (2004)
6. Simossis, V.A., Heringa, J.: PRALINE: A multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Research 33(suppl. 2), W289-W294 (2005)
7. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G.: The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25(24), 4876-4882 (1997)
8. Catalyurek, U., Stahlberg, E., Ferreira, R., Saltzt, J.: Improving Performance of Multiple Sequence Alignment Analysis in Multi-client Environments. In: Proceedings of the First International Workshop on High Performance Computational Biology 2002 (HiCOMB 2002, IPDPS 2002) (2002)
9. Catalyurek, U., Gray, M., Kurc, T., Saltzt, J., Stahlberg, E., Ferreira, R.: A componentbased implementation of multiple sequence alignment. In: Proceedings of the ACM Symposium on Applied Computing: 2003, pp. 122-126 (2003)
10. Li, K.-B.: ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 19(12), 1585-1586 (2003)
11. Chaichoompu, K., Kittitornkun, S., Tongsima, S.: MT-ClustalW: Multithreading multiple sequence alignment. In: 20th International Parallel and Distributed Processing Symposium, IPDPS 2006 (2006)
12. Luo, J., Ahmad, I., Ahmed, M., Paul, R.: Parallel multiple sequence alignment with dynamic scheduling. In: International Conference on Information Technology: Coding and Computing, ITCC 2005, pp. 8-13 (2005)
13. Oliver, T., Schmidt, B., Nathan, D., Clemens, R., Maskell, D.: Multiple sequence alignment on an FPGA. In: Proceedings of the International Conference on Parallel and Distributed Systems - ICPADS 2005, pp. 326-330 (2005)
14. Liu, W., Schmidt, B., Voss, G., Muller-Wittig, W.: Streaming Algorithms for Biological Sequence Alignment on GPUs. IEEE Transactions on Parallel and Distributed Systems (2007)
15. Kahle, J.A., Day, M.N., Hofstee, H.P., Johns, C.R., Maeurer, T.R., Shippy, D.: Introduction to the Cell multiprocessor. IBM Journal of Research and Development 49(4-5), 589-604 (2005)
16. Pande, V.: Folding@Home: Using Worldwide distributed computing to break fundamental barriers in molecular simulation. In: Proceedings of the IEEE International Symposium on High Performance Distributed Computing 2006, p. 4 (2006)
17. Sachdeva, V., Kistler, M., Speight, E., Tzeng, T.-H.K.: Exploring the viability of the Cell Broadband Engine for bioinformatics applications. In: IEEE International Parallel and Distributed Processing Symposium 2007, 8 p. IEEE, Long Beach (2007)
18. Wirawan, A., Kwoh, C.K., Hieu, N.T., Schmidt, B.: CBESW: Sequence alignment on the playstation 3. BMC Bioinformatics, 9 (2008)
19. Stamatakis, A., Ludwig, T., Meier, H.: RAxML-II: A program for sequential, parallel and distributed inference of large phylogenetic trees. Concurrency Computation Practice and Experience 17(14), 1705-1723 (2005)
20. Pham, D., Behnen, E., Bolliger, M., Hofstee, H.P., Johns, C., Kahle, J., Kameyama, A., Keaty, J., Le, B., Masubuchi, Y., et al.: The design methodology and implementation of a first-generation CELL processor: a multi-core SoC. In: Proceedings of the IEEE 2005 Custom Integrated Circuits Conference 2005, San Jose, CA, USA, pp. 45-49. IEEE, Los Alamitos (2005)
21. International Business Machines: Software Development Kit 2.1 Accelerated Library Framework Programmer's Guide and API Reference, Version 1.1. In: IBM developer Works (2007)
22. Feng, D.F., Doolittle, R.F.: Progressive sequence alignment as a prerequisitetto correct phylogenetic trees. Journal of Molecular Evolution 25(4), 351-360 (1987)
23. Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution 4(4), 406-425 (1987)
24. IBM: C/C++ Language Extensions for Cell Broadband Engine Architecture v. 2.5. In. IBM developerWorks (2008)