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A survey of practical algorithms for suffix tree construction in external memory

https://doi.org/10.1002/spe.960
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1097-024x(199911)29:13<1149::aid-spe274>3.0.co;2-oopenalex-snapshot
Reducing the space requirement of suffix trees
inferredcites →https://doi.org/10.1002/spe.535openalex-snapshot
Efficient implementation of lazy suffix trees
inferredcites →https://doi.org/10.1007/3-540-44888-8_14openalex-snapshot
Linear-Time Construction of Suffix Arrays
inferredcites →https://doi.org/10.1007/3-540-44888-8_6openalex-snapshot
Distributed and Paged Suffix Trees for Large Genetic Databases
inferredcites →https://doi.org/10.1007/3-540-45061-0_73openalex-snapshot
Simple Linear Work Suffix Array Construction
inferredcites →https://doi.org/10.1007/3-540-48194-x_17openalex-snapshot
Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications
inferredcites →https://doi.org/10.1007/3-540-48452-3_13openalex-snapshot
A New Indexing Method for Approximate String Matching
inferredcites →https://doi.org/10.1007/3-540-61258-0_9openalex-snapshot
Suffix trees on words
inferredcites →https://doi.org/10.1007/3-540-61440-0_158openalex-snapshot
Optimal logarithmic time randomized suffix tree construction
inferredcites →https://doi.org/10.1007/978-3-540-27810-8_32openalex-snapshot
Two Space Saving Tricks for Linear Time LCP Array Computation
inferredcites →https://doi.org/10.1007/978-3-540-69068-9_16openalex-snapshot
An(other) Entropy-Bounded Compressed Suffix Tree
inferredcites →https://doi.org/10.1007/978-3-540-69068-9_19openalex-snapshot
Dynamic Fully-Compressed Suffix Trees
inferredcites →https://doi.org/10.1007/978-3-540-72845-0_17openalex-snapshot
Engineering a Compressed Suffix Tree Implementation
inferredcites →https://doi.org/10.1007/978-3-642-02927-1_29openalex-snapshot
On Cartesian Trees and Range Minimum Queries
inferredcites →https://doi.org/10.1007/978-3-642-03784-9_7openalex-snapshot
Compressed Suffix Arrays for Massive Data
inferredcites →https://doi.org/10.1007/bf01185207openalex-snapshot
Algorithms for parallel memory, I: Two-level memories
inferredcites →https://doi.org/10.1007/bf01206331openalex-snapshot
On-line construction of suffix trees
inferredcites →https://doi.org/10.1007/pl00009177openalex-snapshot
From Ukkonen to McCreight and Weiner: A Unifying View of Linear-Time Suffix Tree Construction
inferredcites →https://doi.org/10.1007/s00224-006-1198-xopenalex-snapshot
Compressed Suffix Trees with Full Functionality
inferredcites →https://doi.org/10.1007/s00453-001-0051-5openalex-snapshot
A Theoretical and Experimental Study on the Construction of Suffix Arrays in External Memory
inferredcites →https://doi.org/10.1007/s00453-004-1094-1openalex-snapshot
Engineering a Lightweight Suffix Array Construction Algorithm
inferredcites →https://doi.org/10.1007/s00778-005-0154-8openalex-snapshot
Practical methods for constructing suffix trees
inferredcites →https://doi.org/10.1016/0196-6774(92)90049-iopenalex-snapshot
Self-alignments in words and their applications
inferredcites →https://doi.org/10.1016/b978-012088469-8.50007-3openalex-snapshot
Practical Suffix Tree Construction
inferredcites →https://doi.org/10.1016/j.jda.2004.08.002openalex-snapshot
Space efficient linear time construction of suffix arrays
inferredcites →https://doi.org/10.1016/j.jda.2004.08.004openalex-snapshot
Distributed suffix trees
inferredcites →https://doi.org/10.1016/j.tcs.2007.07.017openalex-snapshot
Faster suffix sorting
inferredcites →https://doi.org/10.1017/cbo9780511574931.009openalex-snapshot
First Applications of Suffix Trees
inferredcites →https://doi.org/10.1093/bioinformatics/15.5.426openalex-snapshot
REPuter: fast computation of maximal repeats in complete genomes.
inferredcites →https://doi.org/10.1093/bioinformatics/btl681openalex-snapshot
Compressed suffix tree—a basis for genome-scale sequence analysis
inferredcites →https://doi.org/10.1093/comjnl/17.4.324openalex-snapshot
The Art of Computer Programming, Volume 3, Sorting and Searching
inferredcites →https://doi.org/10.1093/nar/gkj157openalex-snapshot
GenBank
inferredcites →https://doi.org/10.1104/pp.106.084319openalex-snapshot
The TATA-Box Sequence in the Basal Promoter Contributes to Determining Light-Dependent Gene Expression in Plants
inferredcites →https://doi.org/10.1109/icde.2004.1320040openalex-snapshot
Engineering a fast online persistent suffix tree construction
inferredcites →https://doi.org/10.1109/icdm.2008.32openalex-snapshot
Space Efficient String Mining under Frequency Constraints
inferredcites →https://doi.org/10.1109/sfcs.2003.1238199openalex-snapshot
Breaking a time-and-space barrier in constructing full-text indices
inferredcites →https://doi.org/10.1109/swat.1973.13openalex-snapshot
Linear pattern matching algorithms
inferredcites →https://doi.org/10.1137/0206024openalex-snapshot
Fast Pattern Matching in Strings
inferredcites →https://doi.org/10.1137/0222058openalex-snapshot
Suffix Arrays: A New Method for On-Line String Searches
inferredcites →https://doi.org/10.1145/12130.12152openalex-snapshot
Introducing efficient parallelism into approximate string matching and a new serial algorithm
inferredcites →https://doi.org/10.1145/1217856.1217858openalex-snapshot
Linear work suffix array construction
inferredcites →https://doi.org/10.1145/1227161.1402296openalex-snapshot
Better external memory suffix array construction
inferredcites →https://doi.org/10.1145/1242471.1242472openalex-snapshot
A taxonomy of suffix array construction algorithms
inferredcites →https://doi.org/10.1145/1247480.1247572openalex-snapshot
Genome-scale disk-based suffix tree indexing
inferredcites →https://doi.org/10.1145/1458082.1458170openalex-snapshot
A new method for indexing genomes using on-disk suffix trees
inferredcites →https://doi.org/10.1145/1536616.1536632openalex-snapshot
The pathologies of big data
inferredcites →https://doi.org/10.1145/1559845.1559931openalex-snapshot
Serial and parallel methods for i/o efficient suffix tree construction
inferredcites →https://doi.org/10.1145/296854.277632openalex-snapshot
Inverted files versus signature files for text indexing
inferredcites →https://doi.org/10.1145/301970.301973openalex-snapshot
The string B-tree
inferredcites →https://doi.org/10.1145/321479.321481openalex-snapshot
PATRICIA—Practical Algorithm To Retrieve Information Coded in Alphanumeric
inferredcites →https://doi.org/10.1145/321941.321946openalex-snapshot
A Space-Economical Suffix Tree Construction Algorithm
inferredcites →https://doi.org/10.1145/355541.355547openalex-snapshot
On the sorting-complexity of suffix tree construction
inferredcites →https://doi.org/10.1145/359842.359859openalex-snapshot
A fast string searching algorithm
inferredcites →https://doi.org/10.1145/384192.384193openalex-snapshot
External memory algorithms and data structures
inferredcites →https://doi.org/10.1145/48529.48535openalex-snapshot
The input/output complexity of sorting and related problems
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot
Versatile and open software for comparing large genomes
inferredcites →https://doi.org/10.1371/journal.pbio.0030007openalex-snapshot
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development
inferredcites →https://doi.org/10.5555/313651.313681openalex-snapshot
External-memory graph algorithms

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-1-4939-2864-4_413openalex-snapshot
Suffix Tree Construction in Hierarchical Memory
inferred← citeshttps://doi.org/10.1007/978-3-030-75836-3_13openalex-snapshot
Sequential Representation of Suffix Trie: An Empirical Evaluation
inferred← citeshttps://doi.org/10.1007/978-3-031-21534-6openalex-snapshot
Algorithms for Big Data
inferred← citeshttps://doi.org/10.1007/978-3-031-21534-6_14openalex-snapshot
Scalable Text Index Construction
inferred← citeshttps://doi.org/10.1007/978-3-319-26123-2_30openalex-snapshot
Text Analysis with Enhanced Annotated Suffix Trees: Algorithms and Implementation
inferred← citeshttps://doi.org/10.1007/978-3-642-22825-4_8openalex-snapshot
Efficiently Querying Protein Sequences with the Proteinus Index
inferred← citeshttps://doi.org/10.1007/978-3-642-27848-8_413-2openalex-snapshot
Suffix-Tree Construction in Hierarchical Memory
inferred← citeshttps://doi.org/10.1093/bioinformatics/btr483openalex-snapshot
PTPan—overcoming memory limitations in oligonucleotide string matching for primer/probe design
inferred← citeshttps://doi.org/10.1093/nar/gks408openalex-snapshot
Prospects and limitations of full-text index structures in genome analysis
inferred← citeshttps://doi.org/10.3390/bdcc9100258openalex-snapshot
Data Organisation for Efficient Pattern Retrieval: Indexing, Storage, and Access Structures
inferred← citeshttps://doi.org/10.5445/ir/1000085031openalex-snapshot
Scalable String and Suffix Sorting: Algorithms, Techniques, and Tools
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