Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
High-order entropy-compressed text indexes
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Opportunistic data structures with applications
FOCS '00 Proceedings of the 41st Annual Symposium on Foundations of Computer Science
Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
Fast and space efficient string kernels using suffix arrays
ICML '06 Proceedings of the 23rd international conference on Machine learning
ACM Computing Surveys (CSUR)
A taxonomy of suffix array construction algorithms
ACM Computing Surveys (CSUR)
Compressed Suffix Trees with Full Functionality
Theory of Computing Systems
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
A Compressed Enhanced Suffix Array Supporting Fast String Matching
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Faster entropy-bounded compressed suffix trees
Theoretical Computer Science
Parallel and distributed compressed indexes
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Succincter text indexing with wildcards
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
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
Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Bidirectional search in a string with wavelet trees and bidirectional matching statistics
Information and Computation
Lightweight LCP construction for next-generation sequencing datasets
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Computing the longest common prefix array based on the Burrows-Wheeler transform
Journal of Discrete Algorithms
Journal of Discrete Algorithms
Compressed indexes for text with wildcards
Theoretical Computer Science
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Exact string matching is a problem that computer programmers face on a regular basis, and full-text indexes like the suffix tree or the suffix array provide fast string search over large texts. In the last decade, research on compressed indexes has flourished because the main problem in large-scale applications is the space consumption of the index. Nowadays, the most successful compressed indexes are able to obtain almost optimal space and search time simultaneously. It is known that a myriad of sequence analysis and comparison problems can be solved efficiently with established data structures like the suffix tree or the suffix array, but algorithms on compressed indexes that solve these problem are still lacking at present. Here, we show that matching statistics and maximal exact matches between two strings S1 and S2 can be computed efficiently by matching S2 backwards against a compressed index of S1.