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International Conference on Bioinformatics Research and Development

BIRD 2008: Bioinformatics Research and Development pp 489–498Cite as

LASA: A Tool for Non-heuristic Alignment of Multiple Sequences

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Part of the book series: Communications in Computer and Information Science ((CCIS,volume 13))

Abstract

We have developed a non-heuristic tool (LASA) for the multiple sequence alignment problem (MSA), one of the most important problems in computational molecular biology. It is based on a dynamic programming algorithm for solving a Lagrangian relaxation of an integer linear programming (ILP) formulation for MSA. The objective function that is optimized by LASA models the sum-of-pairs scoring scheme and “truly” affine gap costs. Due to a reformulation w.r.t. additionally introduced variables prior to relaxation we improve the convergence rate dramatically while at the same time being able to solve the Lagrangian problem efficiently. Our experiments show that our implementation LASA outperforms all exact algorithms for the multiple sequence alignment problem. Furthermore, the quality of the alignments ranks among the best computed so far.

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Authors and Affiliations

  1. Max-Planck Institut für Informatik, Campus E1 4, D-66123, Saarbrücken, Germany

    Ernst Althaus & Stefan Canzar

Authors
  1. Ernst Althaus
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  2. Stefan Canzar
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Editor information

Mourad Elloumi Josef Küng Michal Linial Robert F. Murphy Kristan Schneider Cristian Toma

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© 2008 Springer-Verlag Berlin Heidelberg

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Althaus, E., Canzar, S. (2008). LASA: A Tool for Non-heuristic Alignment of Multiple Sequences. In: Elloumi, M., Küng, J., Linial, M., Murphy, R.F., Schneider, K., Toma, C. (eds) Bioinformatics Research and Development. BIRD 2008. Communications in Computer and Information Science, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70600-7_38

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  • DOI: https://doi.org/10.1007/978-3-540-70600-7_38

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-70598-7

  • Online ISBN: 978-3-540-70600-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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