KIT | KIT-Bibliothek | Impressum | Datenschutz

On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching

Fischer, Johannes; Köppl, Dominik; Kurpicz, Florian

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).


Verlagsausgabe §
DOI: 10.5445/IR/1000136561
Veröffentlicht am 20.08.2021
Originalveröffentlichung
DOI: 10.4230/LIPIcs.CPM.2016.26
Scopus
Zitationen: 9
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Proceedingsbeitrag
Publikationsdatum 27.06.2016
Sprache Englisch
Identifikator ISBN: 978-3-9597701-2-5
ISSN: 1868-8969
KITopen-ID: 1000136561
Erschienen in Combinatorial Pattern Matching : 27th Annual Symposium on Combinatorial Pattern Matching, June 27-29, 2016, Tel Aviv, Israel. Ed.: R. Grossi
Veranstaltung 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016), Tel Aviv, Israel, 27.06.2016 – 29.06.2016
Verlag Schloss Dagstuhl - Leibniz-Zentrum für Informatik GmbH (LZI)
Seiten 26:1–26:11
Serie Leibniz International Proceedings in Informatics (LIPIcs) ; 54
Externe Relationen Siehe auch
Nachgewiesen in Scopus
KIT – Die Forschungsuniversität in der Helmholtz-Gemeinschaft
KITopen Landing Page