Improved Filters for the Approximate Suffix-Prefix Overlap Problem

  • Gregory Kucherov
  • Dekel Tsur
Conference paper

DOI: 10.1007/978-3-319-11918-2_14

Volume 8799 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Kucherov G., Tsur D. (2014) Improved Filters for the Approximate Suffix-Prefix Overlap Problem. In: Moura E., Crochemore M. (eds) String Processing and Information Retrieval. SPIRE 2014. Lecture Notes in Computer Science, vol 8799. Springer, Cham

Abstract

Computing suffix-prefix overlaps for a large collection of strings is a fundamental building block for the analysis of genomic next-generation sequencing data. The approximate suffix-prefix overlap problem is to find all pairs of strings from a given set such that a prefix of one string is similar to a suffix of the other. Välimäki et al. (Information and Computation, 2012) gave a solution to this problem based on suffix filters. In this work, we propose two improvements to the method of Välimäki et al. that reduce the running time of the computation.

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Gregory Kucherov
    • 1
    • 2
  • Dekel Tsur
    • 2
  1. 1.CNRS/LIGMUniversité Paris-Est Marne-la-ValléeFrance
  2. 2.Department of Computer ScienceBen-Gurion University of the NegevIsrael