15. Filters and Seeds Approaches for Fast Homology Searches in Large Datasets

  1. Mourad Elloumi4 and
  2. Albert Y. Zomaya5
  1. Nadia Pisanti1,
  2. Mathieu Giraud2 and
  3. Pierre Peterlongo3

Published Online: 23 DEC 2010

DOI: 10.1002/9780470892107.ch15

Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications

Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications

How to Cite

Pisanti, N., Giraud, M. and Peterlongo, P. (2011) Filters and Seeds Approaches for Fast Homology Searches in Large Datasets, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications (eds M. Elloumi and A. Y. Zomaya), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470892107.ch15

Editor Information

  1. 4

    Unit of Technologies of Information and Communication (UTIC) and University of Tunis-El Manar, Tunisia

  2. 5

    School of Information Technologies, The University of Sydney, Australia

Author Information

  1. 1

    Dipartimento di Informatica, University of Pisa, Italy

  2. 2

    LIFL, University of Lille 1 and INRIA Lille - Nord Europe, Villeneuve d'Ascq, France

  3. 3

    INRIA Rennes Bretagne Atlantique, Campus de Beaulieu, Rennes, France

Publication History

  1. Published Online: 23 DEC 2010
  2. Published Print: 18 JAN 2011

ISBN Information

Print ISBN: 9780470505199

Online ISBN: 9780470892107

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Keywords:

  • filters and seeds approaches for fast homology searches in large datasets - homologies, inside large sequences or set of sequences, key to molecular biology studies;
  • lossy seed-based filters, dealing with weaker similarities - lossless filters, difficulty in implementing efficiently;
  • sequence homologies, key to molecular biology studies - modeled by approximate repeats and approximate multiple repeats

Summary

This chapter contains sections titled:

  • Introduction

  • Methods Framework

  • Lossless filters

  • Lossy Seed-Based Filters

  • Conclusion

  • Acknowledgments

  • References