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Search Schemes for Approximate Pattern Matching: An Overview

Authors Lore Depuydt , Jan Fostier , Simon Gottlieb , Gregory Kucherov , Knut Reinert , Luca Renders

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ACM Subject Classification
  • Theory of computation → Pattern matching
Keywords
  • FM-index
  • bidirectional index
  • approximate pattern matching
  • search scheme

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Abstract

We provide a brief survey of results on solving the approximate pattern matching problem using search schemes, as introduced by Kucherov et al. (2016). We demonstrate that search schemes constitute a flexible and versatile tool that enable the specification of various search strategies, including several known filtering methods. We present approaches for designing efficient search schemes and for implementing them effectively. Finally, we conclude with experimental results comparing multiple search schemes on DNA sequencing data using the Columba software by Renders et al. (2021).

Cite As Get BibTex

Lore Depuydt, Jan Fostier, Simon Gottlieb, Gregory Kucherov, Knut Reinert, and Luca Renders. Search Schemes for Approximate Pattern Matching: An Overview. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025) https://doi.org/10.4230/OASIcs.Manzini.9

Author Details

Lore Depuydt
  • Department of Information Technology, Ghent University - imec, Belgium
Jan Fostier
  • Department of Information Technology, Ghent University - imec, Belgium
Simon Gottlieb
  • FB Mathematik & Informatik, Freie Universität Berlin, Germany
Gregory Kucherov
  • LIGM, CNRS, Université Gustave Eiffel, Marne-la-Vallée, France
Knut Reinert
  • FB Mathematik & Informatik, Freie Universität Berlin, Germany
Luca Renders
  • Department of Information Technology, Ghent University - imec, Belgium

Funding

  • Depuydt, Lore: Ph.D. Fellowship FR (1117322N), Research Foundation - Flanders (FWO).
  • Renders, Luca: Ph.D. Fellowship SB (1SE7822N), Research Foundation - Flanders (FWO).

Supplementary Materials

References

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