High-speed multiple sequence alignment on a reconfigurable platform

International Journal of Bioinformatics Research and Applications

Volumn 2, Issue 4, 2006, Pages 394-406

  Oliver, Tim ^a   Schmidt, Bertil ^a   Maskell, Douglas ^a   Nathan, Darran ^b   Clemens, Ralf ^b  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b DEPARTMENT OF ELECTRONICS AND COMPUTER ENGINEERING   (Singapore)

Author keywords

Bioinformatics research and applications; CtustalW; fine grained parallelism; FPGA; Multiple Sequence Alignment (MSA); Reconfigurable computing

Indexed keywords

ALGORITHM; COMPUTER PROGRAM; CONFERENCE PAPER; MATHEMATICAL ANALYSIS; PERFORMANCE; SEQUENCE ALIGNMENT; SEQUENCE DATABASE; VELOCITY;

EID: 33846169798     PISSN: 17445458     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2006.011038     Document Type: Conference Paper

References (16)

1. Di Blas, A., Dahle, D., Diekhans, M., Grate, L., Hirschberg, J., Karplus, K., Keller, H., Kendrick, M., Pease, D., Rice, E., Schultz, A., Speck, D. and Hughey, R. (2005) 'The UCSC kestrel parallel processor', IEEE Transactions on Parallel and Distributed Systems, Vol. 16, No. 1, pp.80-92.
2. Duzlevski, O. (2002) SMP version of ClustalW 1.82, unpublished, Available online from http://bioinfo.pbi.nrc.ca/clustalw-smp/.
3. Ebedes, J. and Datta, A. (2004) 'Multiple Sequence Alignment in parallel on a workstation cluster', Bioinformatics, Vol. 20, No. 7, pp.1193-1195.
4. Edgar, R.C. (2004) 'MUSCLE: Multiple Sequence Alignment with high accuracy and high throughput', Nucleic Acid Research, Vol. 32, No. 5, pp.1792-1797.
5. Feng, D.F. and Doolittle, R.F. (1987) 'Progressive sequence alignment as a prerequisite to a correct phylogenetic trees', Journal of Molecular Evolution, Vol. 25, pp.351-360.
6. Guerdoux-Jamet, P. and Lavenier, D. (1997) 'SAMBA: hardware accelerator for biological sequence comparison', CABIOS, Vol. 12, No. 6, pp.609-615.
7. Heringa, J. (1999) 'Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment', Comput. Chem., Vol. 23, pp.341-364.
8. Hughey, R. (1996) 'Parallel hardware for sequence comparison and alignment', CABIOS, Vol. 12, No. 6, pp.473-479.
9. Kleinjung, J., Douglas, N. and Heringa, J. (2002) 'Parallelized Multiple Sequence Alignment', Bioinformatics, Vol. 18, No. 9, pp.1270-1281.
10. Li, K.B. (2003) 'ClustalW-MPI: ClustalW analysis using parallel and distributed computing', Bioinformatics, Vol. 19, No. 12, pp.1585-1586.
11. Mikhailov, D., Cofer, H. and Gomperts, R. (2001) 'Performance optimization of ClustalW: parallel ClustalW, HT Clustal, and MULTICLUSTAL', White Papers, Silicon Graphics, CA.
12. Notredame, C., Higgins, D.G. and Heringa, J. (2000) 'T-Coffee: a novel method for fast and accurate Multiple Sequence Alignment', Journal of Molecular Biology, Vol. 302, No. 1, pp.205-217.
13. Saitou, N. and Nei, M. (1987) 'The neighbour-joining method: a new method for reconstructing phylogenetic trees', Mol. Biol. Evol., Vol. 4, pp.406-425.
14. Schmidt, B., Schröder, H. and Schimmler, M (2002) 'Massively parallel solutions for molecular sequence analysis', Proceedings 15th IEEE International Parallel and Distributed Processing Symposium 2002 (IPDPS), Fort Lauderdale, Fl, pp.186-193.
15. Smith, T.F. and Waterman, M.S. (1981) 'Identification of common molecular subsequences', Journal of Molecular Biology, Vol. 147, pp.195-197.
16. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) 'ClustalW: improving the sensitivity of progressive Multiple Sequence Alignment through sequence weighting position specific gap penalties and weight matrix choice', Nucleic Acids Res., Vol. 22, pp.4673-4680.