Abstract

We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms and their complexities. We present a number of experiments to compare the performance of the different algorithms and show which are the best choices according to each case. We conclude with some future work directions and open problems. 1

Citations

8980	Introduction to Algorithmics - Cormen, Leiserson, et al. - 2001
4787	Basic local alignment search tool - Altschul, Gish, et al. - 1990
4091	Introduction to Automata Theory, Languages, and Computation - HOPCROFT, ULLMAN - 1979
2634	Modern Information Retrieval - Baeza-Yates, Ribeiro-Neto - 1999
2541	The Design and Analysis of Computer Algorithms - Aho, Hopcroft, et al. - 1974
1563	A general method applicable to the search for similarities in the amino acid sequence of two proteins - Needleman, Wunsch - 1970
1330	Binary codes capable of correcting deletions, insertions, and reversals - Levenshtein - 1966
942	Algorithms on Strings, Trees, And Sequences - Gusfield - 1997
737	The Art of Computer Programming, Volume 3: Sorting and Searching - Knuth - 1998
695	The string-to-string correction problem - Wagner, Fischer - 1974
658	Fast pattern matching in strings - Knuth, Morris, et al. - 1977
606	A Fast String Searching Algorithm - Boyer, Moore - 1977
568	Efficient String Matching: An Aid to Bibliographic Search - Aho, Corasick - 1975
564	A space-economical suffix tree construction algorithm - McCreight - 1976
439	Linear pattern matching algorithms - Weiner - 1973
415	Time warps, string edits, and macromolecules: the theory and practice of sequence comparison - Sankoff, Kruskal - 1983
381	Techniques for automatically correcting words in text - Kukich - 1992
341	Fast algorithms for finding nearest common ancestors - Harel, Tarjan - 1984
339	Text Algorithms - Crochemore, Rytter - 1994
331	Fast text searching allowing errors - Wu, Manber - 1992
285	edn). Introduction to Computational Biology - Waterman - 1995
250	On the theory and computation of evolutionary distance - Sellers - 1974
235	A New Approach to Text Searching - Baeza-Yates, Gonnet - 1992
227	A technique for computer detection and correction of spelling errors - Damerau - 1964
216	Accessibility of information on the web - Lawrence, Giles - 1999
200	Glimpse: A tool to search through entire file systems - Manber, Wu
188	On finding lowest common ancestors: Simplification and parallelization - Schieber, Vishkin - 1988
181	A faster algorithm computing string edit distances - Masek, Paterson
171	An O(ND) difference algorithm and its variations - Myers - 1986
168	Approximate string-matching with qgrams and maximal matches. Theoretical Computer Science 92 - Ukkonen - 1992
160	Finding approximate patterns in strings - Ukkonen
146	A fast bit-vector algorithm for approximate string matching based on dynamic programming - Myers - 1999
139	Dowling: Approximate String Matching - Hall, R - 1980
138	Agrep - a fast approximate pattern-matching tool - Wu, Manber
125	The string to string correction problem - Wagner, Fisher - 1974
118	The myriad virtues of subword trees - Apostolico - 1985
114	Fast parallel and serial approximate string matching - Landau, Vishkin - 1989
112	Practical Fast Searching in Strings - Horspool - 1980
109	A very fast substring search algorithm - Sunday - 1990
101	The smallest automaton recognizing the subwords of a text. Theoret - Blumer, Blumer, et al. - 1985
100	Binary codes capable of correcting spurious insertions and deletions of ones - Levenshtein - 1965
98	A sublinear algorithm for approximate keyword searching - Myers - 1994
95	W.: Speeding up two string matching algorithms. Algorithmica 12 - Crochemore, Czumaj, et al. - 1994
89	A string matching algorithm fast on the average - Commentz-Walter - 1979
89	Transducers and repetitions - Crochemore - 1986
81	An improved algorithm for approximate string matching - Galil, Park - 1989
79	Patricia--practical algorithm to retrieve information coded in alphanumeric - Morrison - 1968
77	The string-to-string correction problem with block moves - Tichy - 1984
73	Faster approximate string matching - Baeza-Yates, Navarro - 1999
71	Two algorithms for approximate string matching in static texts - Jokinen, Ukkonen - 1991