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Multiple Sequence Alignment Based on Set Covers

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Applications of Evolutionary Computing (EvoWorkshops 2006)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3907))

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Abstract

We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned. These blocks are obtained with the aid of a new data structure, called a suffix-set tree, which is constructed from the input sequences with the guidance of the residue-alphabet set cover and generalizes the well-known suffix tree of the sequence set. We provide performance results on selected BAliBASE amino-acid sequences and compare them with those yielded by some prominent approaches.

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Author information

Authors and Affiliations

  1. Programa de Engenharia de Sistemas e Computação, COPPE, Universidade Federal do Rio de Janeiro, Caixa Postal 68511, Rio de Janeiro, RJ, 21941-972, Brazil

    Alexandre H. L. Porto & Valmir C. Barbosa

Authors
  1. Alexandre H. L. Porto
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  2. Valmir C. Barbosa
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Editor information

Editors and Affiliations

  1. Johannes Gutenberg University, Mainz, Germany

    Franz Rothlauf

  2. Institute AIFB, University of Karlsruhe, 76128, Karlsruhe, Germany

    Jürgen Branke

  3. Dipartimento di Ingegneria dell’Informazione, Università di Parma,  

    Stefano Cagnoni

  4. Centre of Informatics and Systems of the University of Coimbra,  

    Ernesto Costa

  5. Dept. LCC, Universidad de Málaga, Spain

    Carlos Cotta

  6. Institute of Computer Science, University of Bremen, 28359, Bremen, Germany

    Rolf Drechsler

  7. INRIA Saclay - Ile-de-France, Parc Orsay Université, 4, rue Jacques Monod, 91893, ORSAY Cedex, France

    Evelyne Lutton

  8. CISUC, Department of Informatics Engineering, University of Coimbra, Polo II of the University of Coimbra, 3030, Coimbra, Portugal

    Penousal Machado

  9. Dartmouth College, Lebanon, NH, USA

    Jason H. Moore

  10. Universidade de A Coruña, CP 15071, A Coruña, Spain

    Juan Romero

  11. School of Computing Sciences, UEA Norwich, University of East Anglia, NR4 7TJ, Norwich, UK

    George D. Smith

  12. Dipartimento di Automatica e Informatica, Politecnico di Torino, Italy

    Giovanni Squillero

  13. Kyushu University, Japan

    Hideyuki Takagi

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© 2006 Springer-Verlag Berlin Heidelberg

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Porto, A.H.L., Barbosa, V.C. (2006). Multiple Sequence Alignment Based on Set Covers. In: Rothlauf, F., et al. Applications of Evolutionary Computing. EvoWorkshops 2006. Lecture Notes in Computer Science, vol 3907. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11732242_12

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  • DOI: https://doi.org/10.1007/11732242_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-33237-4

  • Online ISBN: 978-3-540-33238-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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