On finding lowest common ancestors: simplification and parallelization
SIAM Journal on Computing
Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
A generalized suffix tree and its (un)expected asymptotic behaviors
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
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing
Reducing the space requirement of suffix trees
Software—Practice & Experience
Average Case Analysis of Algorithms on Sequences
Average Case Analysis of Algorithms on Sequences
The Enhanced Suffix Array and Its Applications to Genome Analysis
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Optimal Exact Strring Matching Based on Suffix Arrays
SPIRE 2002 Proceedings of the 9th International Symposium on String Processing and Information Retrieval
Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Color Set Size Problem with Application to String Matching
CPM '92 Proceedings of the Third Annual Symposium on Combinatorial Pattern Matching
Engineering a Lightweight Suffix Array Construction Algorithm
ESA '02 Proceedings of the 10th Annual European Symposium on Algorithms
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
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
Optimized relative Lempel-Ziv compression of genomes
ACSC '11 Proceedings of the Thirty-Fourth Australasian Computer Science Conference - Volume 113
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We present new algorithms for computing matching statistics with suffix arrays. We show how the Multiple Common Substring Problem can be solved efficiently in practice with a new approach using matching statistics. This problem consists of finding the common substrings of a set of strings. For the computation of matching statistics we compare seven different methods based on suffix trees and suffix arrays. Most of the suffix array algorithms have an inferior asymptotic worst case running time but a very low memory overhead and small constants in the running time complexity. Our experiments show a good performance in practice. Copyright © 2005 John Wiley & Sons, Ltd.