License: 
Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.CPM.2016.26
URN: urn:nbn:de:0030-drops-60669
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2016/6066/
Fischer, Johannes ;
Köppl, Dominik ;
Kurpicz, Florian
On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching
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}
}
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Keywords: |
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parallel algorithms, pattern matching, approximate string matching |
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Collection: |
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27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016) |
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Issue Date: |
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2016 |
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Date of publication: |
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27.06.2016 |
