Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik GmbH Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik GmbH scholarly article en Fischer, Johannes; Köppl, Dominik; Kurpicz, Florian http://www.dagstuhl.de/lipics License
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On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching

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Abstract

We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with p processors. Given a static text of length n, we first show how to compute the suffix array interval of a given pattern of length m in O(m/p + lg p + lg lg p * lg lg n) time for p <= m. For approximate pattern matching with k differences or mismatches, we show how to compute all occurrences of a given pattern in O((m^k sigma^k)/p max (k, lg lg n) + (1+m/p) lg p * lg lg n + occ} time, where sigma is the size of the alphabet and p <= sigma^k m^k. The workhorse of our algorithms is a data structure for merging suffix array intervals quickly: Given the suffix array intervals for two patterns P and P', we present a data structure for computing the interval of PP' in O(lg lg n) sequential time, or in O(1 + lg_p lg n) parallel time. All our data structures are of size O(n) bits (in addition to the suffix array).

BibTeX - Entry

@InProceedings{fischer_et_al:LIPIcs:2016:6066,
  author =	{Johannes Fischer and Dominik K{\"o}ppl and Florian Kurpicz},
  title =	{{On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching}},
  booktitle =	{27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)},
  pages =	{26:1--26:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-012-5},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{54},
  editor =	{Roberto Grossi and Moshe Lewenstein},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2016/6066},
  URN =		{urn:nbn:de:0030-drops-60669},
  doi =		{10.4230/LIPIcs.CPM.2016.26},
  annote =	{Keywords: parallel algorithms, pattern matching, approximate string matching}
}

Keywords: parallel algorithms, pattern matching, approximate string matching
Seminar: 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)
Issue date: 2016
Date of publication: 2016


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