Compact q-gram Profiling of Compressed Strings

Philip Bille, Patrick Hagge Cording, Inge Li Gørtz

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Abstract

We consider the problem of computing the q-gram profile of a string T of size N compressed by a context-free grammar with n production rules. We present an algorithm that runs in O(N − α) expected time and uses O(n + k T , q ) space, where N − α ≤ qn is the exact number of characters decompressed by the algorithm and k T , q  ≤ N − α is the number of distinct q-grams in T . This simultaneously matches the current best known time bound and improves the best known space bound. Our space bound is asymptotically optimal in the sense that any algorithm storing the grammar and the q-gram profile must use Ω(n + k T , q ) space. To achieve this we introduce the q-gram graph that space-efficiently captures the structure of a string with respect to its q-grams, and show how to construct it from a grammar.
Original languageEnglish
Title of host publicationCombinatorial Pattern Matching : 24th Annual Symposium, CPM 2013, Bad Herrenalb, Germany, June 17-19, 2013. Proceedings
PublisherSpringer
Publication date2013
Pages62-73
ISBN (Print)978-3-642-38904-7
ISBN (Electronic)978-3-642-38905-4
DOIs
Publication statusPublished - 2013
Event24th Annual Symposium on Combinatorial Pattern Matching (CPM 2013) - Bad Herrenalb, Germany
Duration: 17 Jun 201319 Jun 2013
http://www.cpm2013.de/

Conference

Conference24th Annual Symposium on Combinatorial Pattern Matching (CPM 2013)
Country/TerritoryGermany
CityBad Herrenalb
Period17/06/201319/06/2013
Internet address
SeriesLecture Notes in Computer Science
Volume7922
ISSN0302-9743

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