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International Workshop on Combinatorial Algorithms

IWOCA 2014: Combinatorial Algorithms pp 364-375 | Cite as

Lossless Seeds for Searching Short Patterns with High Error Rates

  • Christophe Vroland
  • Mikaël Salson
  • Hélène Touzet
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8986)

Abstract

We address the problem of approximate pattern matching using the Levenshtein distance. Given a text T and a pattern P, find all locations in T that differ by at most k errors from P. For that purpose, we propose a filtration algorithm that is based on a novel type of seeds, combining exact parts and parts with a fixed number of errors. Experimental tests show that the method is specifically well-suited for short patterns with a large number of errors.

Keywords

High Error Rate Levenshtein Distance Text Index Space Consumption Short Pattern 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Christophe Vroland
    • 1
    • 2
    • 3
  • Mikaël Salson
    • 1
    • 2
  • Hélène Touzet
    • 1
    • 2
  1. 1.LIFL, UMR CNRS 8022Université Lille 1Villeneuve D’ascqFrance
  2. 2.Inria Lille Nord-EuropeVilleneuve D’ascqFrance
  3. 3.Laboratoire Génétique et Evolution des Populations Végétales, UMR CNRS 8198Université Lille1Villeneuve D’ascqFrance

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