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Accelerating Scalar-Product Based Sequence Alignment using Graphics Processor Units

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Abstract

Alignment is one of the basic operations in molecular biology to compare sequences. The most widely used methods for multiple sequence alignment include scalar-product based alignment of groups of sequences. We show that scalar-product based alignment algorithms can be significantly speeded up by general-purpose computing on a modern commonly available graphics card. Thus the huge computational power of graphics cards can be exploited to develop high performance solutions for multiple sequence alignment.

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Acknowledgements

We would like to thank one of the unknown reviewers for helpful comments. The work of C.S. Bassoy was sponsored by the German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung – BMBF) under grant number 13N9079 and Philips Research Hamburg.

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Authors and Affiliations

  1. Institute of Computer Technology, Hamburg University of Technology, 21071, Hamburg, Germany

    Cem Savas Bassoy, Svetlana Torgasin, Mei Yang & Karl-Heinz Zimmermann

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  1. Cem Savas Bassoy
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  2. Svetlana Torgasin
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  3. Mei Yang
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  4. Karl-Heinz Zimmermann
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Correspondence to Karl-Heinz Zimmermann.

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Bassoy, C.S., Torgasin, S., Yang, M. et al. Accelerating Scalar-Product Based Sequence Alignment using Graphics Processor Units. J Sign Process Syst 61, 117–125 (2010). https://doi.org/10.1007/s11265-009-0409-5

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  • DOI: https://doi.org/10.1007/s11265-009-0409-5

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