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DOI: 10.4230/LIPIcs.CPM.2017.9
On-Line Pattern Matching on Similar Texts

Authors: Roberto Grossi, Costas S. Iliopoulos, Chang Liu, Nadia Pisanti, Solon P. Pissis, Ahmad Retha, Giovanna Rosone, Fatima Vayani, and Luca Versari

Published in: LIPIcs, Volume 78, 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)

Abstract
Pattern matching on a set of similar texts has received much attention, especially recently, mainly due to its application in cataloguing human genetic variation. In particular, many different algorithms have been proposed for the off-line version of this problem; that is, constructing a compressed index for a set of similar texts in order to answer pattern matching queries efficiently. However, the on-line, more fundamental, version of this problem is a rather undeveloped topic. Solutions to the on-line version can be beneficial for a number of reasons; for instance, efficient on-line solutions can be used in combination with partial indexes as practical trade-offs. We make here an attempt to close this gap via proposing two efficient algorithms for this problem. Notably, one of the algorithms requires time linear in the size of the texts' representation, for short patterns. Furthermore, experimental results confirm our theoretical findings in practical terms.
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Roberto Grossi, Costas S. Iliopoulos, Chang Liu, Nadia Pisanti, Solon P. Pissis, Ahmad Retha, Giovanna Rosone, Fatima Vayani, and Luca Versari. On-Line Pattern Matching on Similar Texts. In 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 78, pp. 9:1-9:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{grossi_et_al:LIPIcs.CPM.2017.9,
  author =	{Grossi, Roberto and Iliopoulos, Costas S. and Liu, Chang and Pisanti, Nadia and Pissis, Solon P. and Retha, Ahmad and Rosone, Giovanna and Vayani, Fatima and Versari, Luca},
  title =	{{On-Line Pattern Matching on Similar Texts}},
  booktitle =	{28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)},
  pages =	{9:1--9:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-039-2},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{78},
  editor =	{K\"{a}rkk\"{a}inen, Juha and Radoszewski, Jakub and Rytter, Wojciech},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2017.9},
  URN =		{urn:nbn:de:0030-drops-73379},
  doi =		{10.4230/LIPIcs.CPM.2017.9},
  annote =	{Keywords: string algorithms, pattern matching, degenerate strings, elastic-degenerate strings, on-line algorithms}
}
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