Linear-Time Sequence Comparison Using Minimal Absent Words & Applications

  • Maxime Crochemore
  • Gabriele Fici
  • Robert Mercaş
  • Solon P. Pissis
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9644)

Abstract

Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free techniques, which are based on measures referring to the composition of sequences in terms of their constituent patterns. These measures, such as q-gram distance, are usually computed in time linear with respect to the length of the sequences. In this article, we focus on the complementary idea: how two sequences can be efficiently compared based on information that does not occur in the sequences. A word is an absent word of some sequence if it does not occur in the sequence. An absent word is minimal if all its proper factors occur in the sequence. Here we present the first linear-time and linear-space algorithm to compare two sequences by considering all their minimal absent words. In the process, we present results of combinatorial interest, and also extend the proposed techniques to compare circular sequences.

Keywords

Algorithms on strings Sequence comparison Alignment-free comparison Absent words Forbidden words Circular words 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Maxime Crochemore
    • 1
  • Gabriele Fici
    • 2
  • Robert Mercaş
    • 1
    • 3
  • Solon P. Pissis
    • 1
  1. 1.Department of InformaticsKing’s College LondonLondonUK
  2. 2.Dipartimento di Matematica e InformaticaUniversità di PalermoPalermoItaly
  3. 3.Department of Computer ScienceKiel UniversityKielGermany

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