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International Workshop on Algorithms in Bioinformatics

WABI 2015: Algorithms in Bioinformatics pp 231–242Cite as

A Filtering Approach for Alignment-Free Biosequences Comparison with Mismatches

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9289))

Abstract

Alignment-free approaches for sequence similarity based on substring composition are increasingly attracting interest from the scientific community. In fact, in several contexts, with respect to alignment-based approaches, alignment-free techniques are faster but less accurate. Recently, several studies (e.g. [4, 8, 9]) attempted to bridge the accuracy gap with the introduction of approximate matches in the definition of composition-based distance measures.

In this work we present MissMax, an exact algorithm for the computation of the longest common substring with mismatches between each suffix of a sequence x and a sequence y. This collection of statistics is useful for the computation of two similarity distances that have been recently extended to incorporate approximate matching, namely the longest and the average common substring with k mismatches. Our approach is exact, and it is based on a filtering technique that showed, in a set of preliminary experiments, to substantially reduce the size of the set of potential sites of a longest match.

This research was partially supported by PRIN 20122F8B2.

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Notes

  1. 1.

    Here we use a slightly different notation than the one used in [4].

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Author information

Authors and Affiliations

  1. Department of Information Engineering, University of Padova, Padova, Italy

    Cinzia Pizzi

Authors
  1. Cinzia Pizzi
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Correspondence to Cinzia Pizzi .

Editor information

Editors and Affiliations

  1. University of Maryland, College Park, Maryland, USA

    Mihai Pop

  2. University of Lille, Lille, France

    Hélène Touzet

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Pizzi, C. (2015). A Filtering Approach for Alignment-Free Biosequences Comparison with Mismatches. In: Pop, M., Touzet, H. (eds) Algorithms in Bioinformatics. WABI 2015. Lecture Notes in Computer Science(), vol 9289. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-48221-6_17

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  • DOI: https://doi.org/10.1007/978-3-662-48221-6_17

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-48220-9

  • Online ISBN: 978-3-662-48221-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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