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Parallelization of Multiple Genome Alignment

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High Performance Computing and Communications (HPCC 2005)

Part of the book series: Lecture Notes in Computer Science ((LNCCN,volume 3726))

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Abstract

In this work, we implement a genome alignment system which applies parallelization schemes to the ClustalW algorithm and the interface of database querying. Parallel construction of the distance matrices and parallelization of progressive alignment in the ClustalW algorithm are performed on PC-based Linux cluster with message-passing interface libraries. Achieved experiments show good speedup and significant parallel performance.

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Author information

Authors and Affiliations

  1. Department of Communication Engineering,  

    Yiming Li

  2. Microelectronics and Information Systems Research Center,  

    Yiming Li & Cheng-Kai Chen

  3. Department of Computer and Information Science, National Chiao Tung University, Hsinchu City, Hsinchu, 300, Taiwan

    Cheng-Kai Chen

Authors
  1. Yiming Li
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  2. Cheng-Kai Chen
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Editor information

Editors and Affiliations

  1. Department of Computer Science, St. Francis Xavier University, Antigonish, Canada

    Laurence T. Yang

  2. School of Computer Science/Welsh eScience Centre, Cardiff University, UK

    Omer F. Rana

  3. Dipartimento di Ingegneria dell’ Informazione - Second, University of Naples - Italy, Real Casa dell’Annunziata - via Roma, 29 81031, Aversa (CE), Italy

    Beniamino Di Martino

  4. Computer Science Department, University of Tennessee, 37996-3450, Knoxville, TN, USA

    Jack Dongarra

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© 2005 Springer-Verlag Berlin Heidelberg

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Li, Y., Chen, CK. (2005). Parallelization of Multiple Genome Alignment. In: Yang, L.T., Rana, O.F., Di Martino, B., Dongarra, J. (eds) High Performance Computing and Communications. HPCC 2005. Lecture Notes in Computer Science, vol 3726. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11557654_102

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  • DOI: https://doi.org/10.1007/11557654_102

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-29031-5

  • Online ISBN: 978-3-540-32079-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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