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Annual International Conference on Research in Computational Molecular Biology

RECOMB 2005: Research in Computational Molecular Biology pp 189–203Cite as

Efficient q-Gram Filters for Finding All ε-Matches over a Given Length

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3500))

Abstract

Fast and exact comparison of large genomic sequences remains a challenging task in biosequence analysis. We consider the problem of finding all ε-matches between two sequences, i.e. all local alignments over a given length with an error rate of at most ε. We study this problem theoretically, giving an efficient q-gram filter for solving it. Two applications of the filter are also discussed, in particular genomic sequence assembly and blast-like sequence comparison. Our results show that the method is 25 times faster than blast, while not being heuristic.

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Author information

Authors and Affiliations

  1. International NRW Graduate School in Bioinformatics and Genome Research, Center of Biotechnology, Universität Bielefeld, 33594, Bielefeld, Germany

    Kim R. Rasmussen

  2. Technische Fakultät, Universität Bielefeld, 33594, Bielefeld, Germany

    Jens Stoye

  3. Div. of Computer Science, UC Berkeley, Berkeley, CA, 94720-1776, USA

    Eugene W. Myers

Authors
  1. Kim R. Rasmussen
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  2. Jens Stoye
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  3. Eugene W. Myers
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Editor information

Editors and Affiliations

  1. Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Satoru Miyano

  2. Broad Institute of MIT and Harvard, 320 Charles Street, 02141-2023, Cambridge, MA, USA

    Jill Mesirov

  3. Computational Genomics Laboratory, Department of Bioengineering, Boston University, 44 Cummington St., 02215, Boston, MA, USA

    Simon Kasif

  4. Center for Molecular Biology and Computer Sciecne Department, Brown University, 115 Waterman St., 02912, Providence, RI, USA

    Sorin Istrail

  5. University of California, San Diego, USA

    Pavel A. Pevzner

  6. Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, 90089-2910, Los Angeles, CA, USA

    Michael Waterman

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© 2005 Springer-Verlag Berlin Heidelberg

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Rasmussen, K.R., Stoye, J., Myers, E.W. (2005). Efficient q-Gram Filters for Finding All ε-Matches over a Given Length. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds) Research in Computational Molecular Biology. RECOMB 2005. Lecture Notes in Computer Science(), vol 3500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11415770_15

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  • DOI: https://doi.org/10.1007/11415770_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25866-7

  • Online ISBN: 978-3-540-31950-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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