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Comparison of Exact String Matching Algorithms for Biological Sequences

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Bioinformatics Research and Development (BIRD 2008)

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

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Abstract

Exact matching of single patterns in DNA and amino acid sequences is studied. We performed an extensive experimental comparison of algorithms presented in the literature. In addition, we introduce new variations of earlier algorithms. The results of the comparison show that the new algorithms are efficient in practice.

Supported by the Academy of Finland.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, Helsinki University of Technology, P.O. Box 5400, FI-02015 HUT, Finland

    Petri Kalsi, Hannu Peltola & Jorma Tarhio

Authors
  1. Petri Kalsi
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  2. Hannu Peltola
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  3. Jorma Tarhio
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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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Kalsi, P., Peltola, H., Tarhio, J. (2008). Comparison of Exact String Matching Algorithms for Biological 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_31

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  • DOI: https://doi.org/10.1007/978-3-540-70600-7_31

  • 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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