RECONFIGURABLE COMPUTING IP CORES FOR MULTIPLE SEQUENCE ALIGNMENT

M. Lakka, A. Desarti, G. Chrysos, E. Sotiriades, I. Papaefstathiou, A. Dollas

Abstract

Multiple Sequence Alignment (MSA) is a principal tool in computational molecular biology. MSA is considered to be a very challenging problem as many software implementations suffer from quadratic time performance. Two of the best known MSA algorithms, which offer high accuracy and great speed, are T-Coffee and MAFFT. Reconfigurable technology provides a dramatic reduction of execution time by taking advantage of high parallelism. It also allows for different problem sizing solutions within a generic intellectual property (IP) core. This paper presents the implementation of MAFFT and T-Coffee algorithms on present-day Field Programmable Gate Arrays (FPGAs). The performance of the FPGA systems is compared against software implementations, concluding that the parallelism of reconfigurable technology can offer significant computational power to the bioinformatics community..

References

  1. Thompson, J. D., Higgins, D. G., 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 Research, vol 22, pp. 4673-4690.
  2. Notredame, C., Higgins, D. G., Heringa, J., 2000. TCoffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, vol. 302, issue 1, pp. 205-217.
  3. Katoh, K., Kuma, K., Toh, H., Miyata, T., 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research, vol 33, pp. 511-518.
  4. Edgar, R. C., 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5:113.
  5. Do, C. B., Mahabhashyam, M. S. P., Brudno, M., Batzoglou, S., 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research, vol. 15, pp. 330-340.
  6. Morgenster, B., French, K., Dress, A., Werner, T, 1998. DIALIGN: Finding local similiraties by multiple sequrnce alignment. Bioinformatics, vol. 14, No. 3, pp. 290-294.
  7. Oliver, T., Schmidt, B., Nathan, D., Clemens, R., Maskel, D., 2005. Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. Bioinformatics, vol. 21, No. 16500, pp. 3431-3132.
  8. Lin, X., Peiheng, Z., Dongbo, B., Shengzhong, F., Ninghui, S., 2005. To accelerate Multiple Sequence Alignment using FPGAs. High-Performance Computing in Asia-Pacific Region, pp. 176-180.
  9. Boukerche, A., Correa, J. M., Melo, A. C. M. A., Jacobi, R. P., Rocha, A. F., 2007. An FPGA-based accelerator for multiple biological sequence alignment with DIALIGN. International Conference on High Performance Computing, pp. 71-82.
  10. Masuno, S., Maruyama, T., et al., 2007. An FPGA Implementation of Multiple Sequence Alignment Based on Carrillo-Lipman Method. In Proceedings of Field Programmable Logic and Applications, pp. 489- 492.
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Paper Citation


in Harvard Style

Lakka M., Desarti A., Chrysos G., Sotiriades E., Papaefstathiou I. and Dollas A. (2011). RECONFIGURABLE COMPUTING IP CORES FOR MULTIPLE SEQUENCE ALIGNMENT . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 216-221. DOI: 10.5220/0003167402160221


in Bibtex Style

@conference{bioinformatics11,
author={M. Lakka and A. Desarti and G. Chrysos and E. Sotiriades and I. Papaefstathiou and A. Dollas},
title={RECONFIGURABLE COMPUTING IP CORES FOR MULTIPLE SEQUENCE ALIGNMENT},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={216-221},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003167402160221},
isbn={978-989-8425-36-2},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)
TI - RECONFIGURABLE COMPUTING IP CORES FOR MULTIPLE SEQUENCE ALIGNMENT
SN - 978-989-8425-36-2
AU - Lakka M.
AU - Desarti A.
AU - Chrysos G.
AU - Sotiriades E.
AU - Papaefstathiou I.
AU - Dollas A.
PY - 2011
SP - 216
EP - 221
DO - 10.5220/0003167402160221