Linear time construction of compressed text indices in compact space

DOI10.1145/2591796.2591885zbMATH Open1315.68110arXiv1401.0936OpenAlexW1988110322MaRDI QIDQ5259552FDOQ5259552

Djamal Belazzougui

Publication date: 26 June 2015

Published in: Proceedings of the forty-sixth annual ACM symposium on Theory of computing (Search for Journal in Brave)

Abstract: We show that the compressed suffix array and the compressed suffix tree for a string of length $n$ over an integer alphabet of size $sigmaleqn$ can both be built in $O(n)$ (randomized) time using only $O(nlogsigma)$ bits of working space. The previously fastest construction algorithms that used $O(nlogsigma)$ bits of space took times $O(nloglogsigma)$ and $O(nlo{g}^{epsilon}n)$ respectively (where $epsilon$ is any positive constant smaller than $1$). In the passing, we show that the Burrows-Wheeler transform of a string of length $n$ over an alphabet of size $sigma$ can be built in deterministic $O(n)$ time and space $O(nlogsigma)$. We also show that within the same time and space, we can carry many sequence analysis tasks and construct some variants of the compressed suffix array and compressed suffix tree.

Full work available at URL: https://arxiv.org/abs/1401.0936

zbMATH Keywords

pattern matchingtext indexingsuccinct space

Mathematics Subject Classification ID

Data structures (68P05) Coding and information theory (compaction, compression, models of communication, encoding schemes, etc.) (aspects in computer science) (68P30) Algorithms on strings (68W32) Computing methodologies for text processing; mathematical typography (68U15)

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Cited In (18)

• Title not available (Why is that?)
• Space-efficient computation of the LCP array from the Burrows-Wheeler transform
• Lightweight merging of compressed indices based on BWT variants
• Flexible indexing of repetitive collections
• Computing the Burrows-Wheeler transform in place and in small space
• Lempel-Ziv factorization powered by space efficient suffix trees
• Space-Efficient Parallel Construction of Succinct Representations of Suffix Tree Topologies
• Fast Compressed Self-Indexes with Deterministic Linear-Time Construction
• Greedy Shortest Common Superstring Approximation in Compact Space
• Title not available (Why is that?)
• Space-efficient construction of compressed suffix trees
• Title not available (Why is that?)
• Lightweight BWT and LCP Merging via the Gap Algorithm
• Parallel computation of the Burrows Wheeler transform in compact space
• Title not available (Why is that?)
• A framework for space-efficient string kernels
• Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended
• Burrows-Wheeler transform and LCP array construction in constant space

Uses Software

• SuLQ

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