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International Symposium on String Processing and Information Retrieval

SPIRE 2008: String Processing and Information Retrieval pp 99–108Cite as

Mismatch Sampling

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5280))

Abstract

We consider the well known problem of pattern matching under the Hamming distance. Previous approaches have shown how to count the number of mismatches efficiently, especially when a bound is known for the maximum Hamming distance. Our interest is different in that we wish collect a random sample of mismatches of fixed size at each position in the text. Given a pattern p of length m and a text t of length n, we show how to sample with high probability c mismatches where possible from every alignment of p and t in O((c + logn)(n + mlogm)logm) time. Further, we guarantee that the mismatches are sampled uniformly and can therefore be seen as representative of the types of mismatches that occur.

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References

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Author information

Authors and Affiliations

  1. Dept. of Computer Science, University of Bristol, Bristol, BS8 1UB, UK

    Raphaël Clifford

  2. Dept. of Computer Science, 52900 Ramat-Gan, Israel and Weizman institute, Dept. of Computer Science and Applied Mathematics, Bar-Ilan University, Rehovot, Israel

    Klim Efremenko

  3. Dept. of Computer Science, Bar-Ilan University, 52900, Ramat-Gan, Israel

    Benny Porat & Ely Porat

  4. Dept. of computer science, Tel-Aviv, Israel and Bar-Ilan University, Dept. of Computer Science, Tel-Aviv University, 52900, Ramat-Gan, Israel

    Amir Rothschild

Authors
  1. Raphaël Clifford
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  2. Klim Efremenko
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  3. Benny Porat
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  4. Ely Porat
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  5. Amir Rothschild
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Editor information

Editors and Affiliations

  1. Department of Computer Science, Bar-Ilan University, 52900, Ramat-Gan, Israel

    Amihood Amir

  2. School of Computer Science and Information Technology, RMIT University, Melbourne, Australia

    Andrew Turpin

  3. NICTA Victoria Laboratory, Department of Computer Science and Software Engineering, The University of Melbourne, Victoria, Australia

    Alistair Moffat

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© 2008 Springer-Verlag Berlin Heidelberg

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Clifford, R., Efremenko, K., Porat, B., Porat, E., Rothschild, A. (2008). Mismatch Sampling. In: Amir, A., Turpin, A., Moffat, A. (eds) String Processing and Information Retrieval. SPIRE 2008. Lecture Notes in Computer Science, vol 5280. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-89097-3_11

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  • DOI: https://doi.org/10.1007/978-3-540-89097-3_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-89096-6

  • Online ISBN: 978-3-540-89097-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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