Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
Software—Practice & Experience
The string B-tree: a new data structure for string search in external memory and its applications
Journal of the ACM (JACM)
Fast algorithms for sorting and searching strings
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Suffix arrays: a new method for on-line string searches
SODA '90 Proceedings of the first annual ACM-SIAM symposium on Discrete algorithms
Reducing the space requirement of suffix trees
Software—Practice & Experience
Proceedings of the 16th Conference on Foundations of Software Technology and Theoretical Computer Science
Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
On the Performance of BWT Sorting Algorithms
DCC '00 Proceedings of the Conference on Data Compression
Optimal suffix tree construction with large alphabets
FOCS '97 Proceedings of the 38th Annual Symposium on Foundations of Computer Science
Rapid identification of repeated patterns in strings, trees and arrays
STOC '72 Proceedings of the fourth annual ACM symposium on Theory of computing
An Efficient Method for in Memory Construction of Suffix Arrays
SPIRE '99 Proceedings of the String Processing and Information Retrieval Symposium & International Workshop on Groupware
A Fast Algorithms for Making Suffix Arrays and for Burrows-Wheeler Transformation
DCC '98 Proceedings of the Conference on Data Compression
Breaking a Time-and-Space Barrier in Constructing Full-Text Indices
FOCS '03 Proceedings of the 44th Annual IEEE Symposium on Foundations of Computer Science
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
Cache-conscious sorting of large sets of strings with dynamic tries
Journal of Experimental Algorithmics (JEA)
Antisequential Suffix Sorting for BWT-Based Data Compression
IEEE Transactions on Computers
The Performance of Linear Time Suffix Sorting Algorithms
DCC '05 Proceedings of the Data Compression Conference
Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching
SIAM Journal on Computing
ACM Computing Surveys (CSUR)
Linear work suffix array construction
Journal of the ACM (JACM)
An efficient, versatile approach to suffix sorting
Journal of Experimental Algorithmics (JEA)
Fast lightweight suffix array construction and checking
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Linear-time construction of suffix arrays
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Space efficient linear time construction of suffix arrays
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Simple linear work suffix array construction
ICALP'03 Proceedings of the 30th international conference on Automata, languages and programming
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
ACM Computing Surveys (CSUR)
SIGIR '07 Proceedings of the 30th annual international ACM SIGIR conference on Research and development in information retrieval
An efficient, versatile approach to suffix sorting
Journal of Experimental Algorithmics (JEA)
Theoretical Computer Science
Fast BWT in small space by blockwise suffix sorting
Theoretical Computer Science
Improving suffix array locality for fast pattern matching on disk
Proceedings of the 2008 ACM SIGMOD international conference on Management of data
An Alignment-Free Distance Measure for Closely Related Genomes
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Compressed text indexes: From theory to practice
Journal of Experimental Algorithmics (JEA)
A new method for indexing genomes using on-disk suffix trees
Proceedings of the 17th ACM conference on Information and knowledge management
Engineering Radix Sort for Strings
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
Linear Time Suffix Array Construction Using D-Critical Substrings
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Permuted Longest-Common-Prefix Array
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Transformation of Suffix Arrays into Suffix Trees on the MPI Environment
RSFDGrC '07 Proceedings of the 11th International Conference on Rough Sets, Fuzzy Sets, Data Mining and Granular Computing
A four-stage algorithm for updating a Burrows-Wheeler transform
Theoretical Computer Science
Rank/select on dynamic compressed sequences and applications
Theoretical Computer Science
A Compressed Enhanced Suffix Array Supporting Fast String Matching
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Compressed Suffix Arrays for Massive Data
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Information Processing Letters
Faster Algorithms for Computing Maximal Multirepeats in Multiple Sequences
Fundamenta Informaticae - Special Issue on Stringology
Dynamic extended suffix arrays
Journal of Discrete Algorithms
Computing longest common substrings via suffix arrays
CSR'08 Proceedings of the 3rd international conference on Computer science: theory and applications
The compressed permuterm index
ACM Transactions on Algorithms (TALG)
Bidirectional search in a string with wavelet trees
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Medium-space algorithms for inverse BWT
ESA'10 Proceedings of the 18th annual European conference on Algorithms: Part I
Computing matching statistics and maximal exact matches on compressed full-text indexes
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
On the possible patterns of inputs for block sorting in the Burrows-Wheeler transformation
Information Processing Letters
Foundations and Trends in Databases
A quick tour on suffix arrays and compressed suffix arrays
Theoretical Computer Science
Succinct nearest neighbor search
Proceedings of the Fourth International Conference on SImilarity Search and APplications
Lempel-Ziv factorization revisited
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Lightweight BWT construction for very large string collections
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
PSAEC: an improved algorithm for short read error correction using partial suffix arrays
FAW-AAIM'11 Proceedings of the 5th joint international frontiers in algorithmics, and 7th international conference on Algorithmic aspects in information and management
An efficient hybrid approach to correcting errors in short reads
MDAI'11 Proceedings of the 8th international conference on Modeling decisions for artificial intelligence
WADS'11 Proceedings of the 12th international conference on Algorithms and data structures
Indexing finite language representation of population genotypes
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
ERA: efficient serial and parallel suffix tree construction for very long strings
Proceedings of the VLDB Endowment
Computing the longest common prefix array based on the burrows-wheeler transform
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
On the number of elements to reorder when updating a suffix array
Journal of Discrete Algorithms
Bidirectional search in a string with wavelet trees and bidirectional matching statistics
Information and Computation
On-line suffix tree construction with reduced branching
Journal of Discrete Algorithms
Memory-Aware BWT by segmenting sequences to support subsequence search
APWeb'12 Proceedings of the 14th Asia-Pacific international conference on Web Technologies and Applications
Revisiting bounded context block-sorting transformations
Software—Practice & Experience
Efficient in-memory top-k document retrieval
SIGIR '12 Proceedings of the 35th international ACM SIGIR conference on Research and development in information retrieval
Minimum Unique Substrings and Maximum Repeats
Fundamenta Informaticae - Theory that Counts: To Oscar Ibarra on His 70th Birthday
Faster Algorithms for Computing Maximal Multirepeats in Multiple Sequences
Fundamenta Informaticae - Special Issue on Stringology
Computing the burrows-wheeler transform of a string and its reverse
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
A comparison of index-based lempel-Ziv LZ77 factorization algorithms
ACM Computing Surveys (CSUR)
Computing regularities in strings: A survey
European Journal of Combinatorics
Fast and practical algorithms for computing all the runs in a string
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Optimal lightweight construction of suffix arrays for constant alphabets
WADS'07 Proceedings of the 10th international conference on Algorithms and Data Structures
Space-Efficient computation of maximal and supermaximal repeats in genome sequences
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
Parallel suffix array construction for shared memory architectures
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
Computing the longest common prefix array based on the Burrows-Wheeler transform
Journal of Discrete Algorithms
Parallel suffix array and least common prefix for the GPU
Proceedings of the 18th ACM SIGPLAN symposium on Principles and practice of parallel programming
Lightweight algorithms for constructing and inverting the BWT of string collections
Theoretical Computer Science
Trends in suffix sorting: a survey of low memory algorithms
ACSC '12 Proceedings of the Thirty-fifth Australasian Computer Science Conference - Volume 122
Practical linear-time O(1)-workspace suffix sorting for constant alphabets
ACM Transactions on Information Systems (TOIS)
Suffix Array Construction in External Memory Using D-Critical Substrings
ACM Transactions on Information Systems (TOIS)
Indexing Word Sequences for Ranked Retrieval
ACM Transactions on Information Systems (TOIS)
Faster semi-external suffix sorting
Information Processing Letters
A Compressed Suffix Tree Based Implementation With Low Peak Memory Usage
Electronic Notes in Theoretical Computer Science (ENTCS)
Computing the Burrows-Wheeler transform of a string and its reverse in parallel
Journal of Discrete Algorithms
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In 1990, Manber and Myers proposed suffix arrays as a space-saving alternative to suffix trees and described the first algorithms for suffix array construction and use. Since that time, and especially in the last few years, suffix array construction algorithms have proliferated in bewildering abundance. This survey paper attempts to provide simple high-level descriptions of these numerous algorithms that highlight both their distinctive features and their commonalities, while avoiding as much as possible the complexities of implementation details. New hybrid algorithms are also described. We provide comparisons of the algorithms' worst-case time complexity and use of additional space, together with results of recent experimental test runs on many of their implementations.