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Authors: M. Lakka ; A. Desarti ; G. Chrysos ; E. Sotiriades ; I. Papaefstathiou and A. Dollas

Affiliation: Technical University of Crete, Greece

Keyword(s): Multiple Sequence Alignment, Reconfigurable Architecture, Bioinformatics.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Sequence Analysis

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..

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Paper citation in several formats:
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 (BIOSTEC 2011) - BIOINFORMATICS; ISBN 978-989-8425-36-2; ISSN 2184-4305, SciTePress, pages 216-221. DOI: 10.5220/0003167402160221

@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 (BIOSTEC 2011) - BIOINFORMATICS},
year={2011},
pages={216-221},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003167402160221},
isbn={978-989-8425-36-2},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS
TI - RECONFIGURABLE COMPUTING IP CORES FOR MULTIPLE SEQUENCE ALIGNMENT
SN - 978-989-8425-36-2
IS - 2184-4305
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
PB - SciTePress

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