Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
A fast bit-vector algorithm for approximate string matching based on dynamic programming
Journal of the ACM (JACM)
Reducing the space requirement of suffix trees
Software—Practice & Experience
Very fast and simple approximate string matching
Information Processing Letters
A guided tour to approximate string matching
ACM Computing Surveys (CSUR)
An analysis of the Burrows—Wheeler transform
Journal of the ACM (JACM)
Approximate String-Matching over Suffix Trees
CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
Approximate String Matching and Local Similarity
CPM '94 Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching
Filtration with q-Samples in Approximate String Matching
CPM '96 Proceedings of the 7th Annual Symposium on Combinatorial Pattern Matching
Indexing text using the Ziv-Lempel trie
Journal of Discrete Algorithms - SPIRE 2002
New text indexing functionalities of the compressed suffix arrays
Journal of Algorithms
Dictionary matching and indexing with errors and don't cares
STOC '04 Proceedings of the thirty-sixth annual ACM symposium on Theory of computing
Average-optimal single and multiple approximate string matching
Journal of Experimental Algorithmics (JEA)
Journal of the ACM (JACM)
Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching
SIAM Journal on Computing
ACM Computing Surveys (CSUR)
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
A linear size index for approximate pattern matching
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Reducing the space requirement of LZ-Index
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
A compressed self-index using a ziv-lempel dictionary
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
Dotted suffix trees a structure for approximate text indexing
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
Improved approximate string matching using compressed suffix data structures
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
Implementing the LZ-index: Theory versus practice
Journal of Experimental Algorithmics (JEA)
Indexed Hierarchical Approximate String Matching
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
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A compressed full-text self-index for a text T is a data structure requiring reduced space and able of searching for patterns P in T. Furthermore, the structure can reproduce any substring of T, thus it actually replaces T. Despite the explosion of interest on self-indexes in recent years, there has not been much progress on search functionalities beyond the basic exact search. In this paper we focus on indexed approximate string matching (ASM), which is of great interest, say, in computational biology applications. We present an ASM algorithm that works on top of a Lempel-Ziv self-index. We consider the so-called hybrid indexes, which are the best in practice for this problem. We show that a Lemplel-Ziv index can be seen as an extension of the classical q-samples index. We give new insights on this type of index, which can be of independent interest, and then apply them to the Lempel-Ziv index. We show experimentally that our algorithm has a competitive performance and provides a useful space-time tradeoff compared to classical indexes.