Replacing suffix trees with enhanced suffix arrays
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Publication:876707
DOI10.1016/S1570-8667(03)00065-0zbMATH Open1115.92303WikidataQ56485241 ScholiaQ56485241MaRDI QIDQ876707FDOQ876707
Authors: Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch 
Publication date: 26 April 2007
Published in: Journal of Discrete Algorithms (Search for Journal in Brave)
Recommendations
Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20) Searching and sorting (68P10) Computational methods for problems pertaining to biology (92-08)
Cites Work
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- Linear-time construction of suffix arrays (extended abstract)
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Cited In (87)
- Suffix-sorting via Shannon-Fano-Elias codes
- On parsing optimality for dictionary-based text compression -- the \texttt{Zip} case
- Faster online computation of the succinct longest previous factor array
- Kernel-based machine learning for fast text mining in R
- Practical compressed suffix trees
- String Processing and Information Retrieval
- Title not available (Why is that?)
- Faster entropy-bounded compressed suffix trees
- Converting suffix trees into factor/suffix oracles
- LCP array construction in external memory
- Space efficient linear time construction of suffix arrays
- Fast profile matching algorithms - A survey
- Searching for smallest grammars on large sequences and application to DNA
- String matching with alphabet sampling
- Computing longest previous factor in linear time and applications
- An external-memory algorithm for string graph construction
- \(xkcd\)-repeats: a new taxonomy of repeats defined by their context diversity
- Title not available (Why is that?)
- Construction of Aho Corasick automaton in linear time for integer alphabets
- Counting suffix arrays and strings
- Computing regularities in strings: a survey
- Efficient algorithms for the all-pairs suffix-prefix problem and the all-pairs substring-prefix problem
- Lightweight LCP construction for very large collections of strings
- Bidirectional search in a string with wavelet trees and bidirectional matching statistics
- Permuted Longest-Common-Prefix Array
- Spectral concepts in genome informational analysis
- Linearized suffix tree: An efficient index data structure with the capabilities of suffix trees and suffix arrays
- From Suffix Trees to Suffix Vectors
- On space efficient two dimensional range minimum data structures
- Locally compressed suffix arrays
- In-place update of suffix array while recoding words
- Large-scale detection of repetitions
- An improved algorithm for the all-pairs suffix-prefix problem
- Wee LCP
- Note on the greedy parsing optimality for dictionary-based text compression
- The exact multiple pattern matching problem solved by a reference tree approach
- Succinct non-overlapping indexing
- Indexing and querying character sets in one- and two-dimensional words
- Using static suffix array in dynamic application: case of text compression by longest first substitution
- A fast algorithm for the all-pairs suffix-prefix problem
- The affix array data structure and its applications to RNA secondary structure analysis
- Efficient construction of a compressed de Bruijn graph for pan-genome analysis
- Succinct Non-overlapping Indexing
- An Online Algorithm for Finding the Longest Previous Factors
- The principles of informational genomics
- DARN! A weighted constraint solver for RNA motif localization
- Finding range minima in the middle: approximations and applications
- Alphabet-independent algorithms for finding context-sensitive repeats in linear time
- Fast, practical algorithms for computing all the repeats in a string
- Suffix trays and suffix trists: structures for faster text indexing
- Longest repeats with a block of \(k\) don't cares
- Motif trie: an efficient text index for pattern discovery with don't cares
- Computing suffix links for suffix trees and arrays
- Lempel-Ziv Factorization Revisited
- Title not available (Why is that?)
- On-line construction of compact suffix vectors and maximal repeats
- Faster compressed suffix trees for repetitive collections
- Tighter bounds for the sum of irreducible LCP values
- Burrows-Wheeler transform and LCP array construction in constant space
- Engineering parallel string sorting
- The longest common substring problem
- Inducing enhanced suffix arrays for string collections
- Full-text indexes for high-throughput sequencing
- Kings, name days, lazy servants and magic
- String Covering: A Survey
- String inference from longest-common-prefix array
- Sliding suffix tree
- Online Suffix Tree Construction for Streaming Sequences
- Crochemore's repetitions algorithm revisited: computing runs
- Faster repetition-aware compressed suffix trees based on block trees
- Property Suffix Array with Applications in Indexing Weighted Sequences
- Engineering a lightweight external memory suffix array construction algorithm
- The virtual suffix tree
- Computational graph pangenomics: a tutorial on data structures and their applications
- Sparse and truncated suffix trees on variable-length codes
- DNA-seq error correction based on substring indices
- Indexing a sequence for mapping reads with a single mismatch
- Better external memory LCP array construction
- Finding all maximal perfect haplotype blocks in linear time
- Faster repetition-aware compressed suffix trees based on block trees
- Optimal in-place suffix sorting
- Space-efficient parallel construction of succinct representations of suffix tree topologies
- Tighter bounds for the sum of irreducible LCP values
- Locating maximal approximate runs in a string
- On succinct representations of binary trees
- On the computation of longest previous non-overlapping factors
- Computing all-vs-all MEMs in grammar-compressed text
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