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International Conference on Computational Science and Its Applications

ICCSA 2004: Computational Science and Its Applications – ICCSA 2004 pp 81–88Cite as

A Useful Method for Multiple Sequence Alignment and Its Implementation

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Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 3043))

Abstract

Multiple sequence alignment is a useful tool to identify the relationships among protein sequences. Dynamic programming is the most widely used algorithm to obtain multiple sequence alignment with optimal cost. However, dynamic programming cannot be applied to certain cost function due to its drawback to produce an optimal multiple sequence alignment. We propose sub-alignment refinement algorithm to overcome this drawback and impelment this algorithm as a module of our MS Windows-based sequence alignment program which also implements other alignment algorithms and supports several sequence file formats.

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Author information

Authors and Affiliations

  1. Division of Information and Communication Engineering, Hallym University, 1 Ockchundong Chunchon, Kangwondo, 200-702, Republic of Korea

    Jin Kim, Dong-Hoi Kim & Saangyong Uhmn

Authors
  1. Jin Kim
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  2. Dong-Hoi Kim
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  3. Saangyong Uhmn
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Editor information

Editors and Affiliations

  1. Department of Chemistry, University of Perugia, Via Elce di Sotto, 8, I-06123, Perugia, Italy

    Antonio Laganá

  2. Department of Computer Science, University of Calgary, 2500 University Drive N.W., T2N 1N4, Calgary, AB, Canada

    Marina L. Gavrilova

  3. William Norris Professor, Head of the Computer Science and Engineering Department, University of Minnesota, USA

    Vipin Kumar

  4. School of Computing, Soongsil University, Seoul, Korea

    Youngsong Mun

  5. OptimaNumerics Ltd., Cathedral House, 23-31 Waring Street, BT1 2DX, Belfast, UK

    C. J. Kenneth Tan

  6. Department of Mathematics and Computer Science, University of Perugia, via Vanvitelli, 1, I-06123, Perugia, Italy

    Osvaldo Gervasi

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© 2004 Springer-Verlag Berlin Heidelberg

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Kim, J., Kim, DH., Uhmn, S. (2004). A Useful Method for Multiple Sequence Alignment and Its Implementation. In: Laganá, A., Gavrilova, M.L., Kumar, V., Mun, Y., Tan, C.J.K., Gervasi, O. (eds) Computational Science and Its Applications – ICCSA 2004. ICCSA 2004. Lecture Notes in Computer Science, vol 3043. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24707-4_11

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  • DOI: https://doi.org/10.1007/978-3-540-24707-4_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-22054-1

  • Online ISBN: 978-3-540-24707-4

  • eBook Packages: Springer Book Archive

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