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129
A Guided Tour to Approximate String Matching
 ACM COMPUTING SURVEYS
, 1999
"... 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 t ..."
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Cited by 598 (36 self)
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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.
OnLine Construction of Suffix Trees
, 1995
"... An online algorithm is presented for constructing the suffix tree for a given string in time linear in the length of the string. The new algorithm has the desirable property of processing the string symbol by symbol from left to right. It has always the suffix tree for the scanned part of the strin ..."
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Cited by 437 (2 self)
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An online algorithm is presented for constructing the suffix tree for a given string in time linear in the length of the string. The new algorithm has the desirable property of processing the string symbol by symbol from left to right. It has always the suffix tree for the scanned part of the string ready. The method is developed as a lineartime version of a very simple algorithm for (quadratic size) suffix tries. Regardless of its quadratic worstcase this latter algorithm can be a good practical method when the string is not too long. Another variation of this method is shown to give in a natural way the wellknown algorithms for constructing suffix automata (DAWGs).
Compressed fulltext indexes
 ACM COMPUTING SURVEYS
, 2007
"... Fulltext indexes provide fast substring search over large text collections. A serious problem of these indexes has traditionally been their space consumption. A recent trend is to develop indexes that exploit the compressibility of the text, so that their size is a function of the compressed text l ..."
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Cited by 263 (94 self)
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Fulltext indexes provide fast substring search over large text collections. A serious problem of these indexes has traditionally been their space consumption. A recent trend is to develop indexes that exploit the compressibility of the text, so that their size is a function of the compressed text length. This concept has evolved into selfindexes, which in addition contain enough information to reproduce any text portion, so they replace the text. The exciting possibility of an index that takes space close to that of the compressed text, replaces it, and in addition provides fast search over it, has triggered a wealth of activity and produced surprising results in a very short time, and radically changed the status of this area in less than five years. The most successful indexes nowadays are able to obtain almost optimal space and search time simultaneously. In this paper we present the main concepts underlying selfindexes. We explain the relationship between text entropy and regularities that show up in index structures and permit compressing them. Then we cover the most relevant selfindexes up to date, focusing on the essential aspects on how they exploit the text compressibility and how they solve efficiently various search problems. We aim at giving the theoretical background to understand and follow the developments in this area.
Replacing suffix trees with enhanced suffix arrays
, 2004
"... The suffix tree is one of the most important data structures in string processing and comparative genomics. However, the space consumption of the suffix tree is a bottleneck in large scale applications such as genome analysis. In this article, we will overcome this obstacle. We will show how every ..."
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Cited by 207 (10 self)
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The suffix tree is one of the most important data structures in string processing and comparative genomics. However, the space consumption of the suffix tree is a bottleneck in large scale applications such as genome analysis. In this article, we will overcome this obstacle. We will show how every algorithm that uses a suffix tree as data structure can systematically be replaced with an algorithm that uses an enhanced suffix array and solves the same problem in the same time complexity. The generic name enhanced suffix array stands for data structures consisting of the suffix array and additional tables. Our new algorithms are not only more space efficient than previous ones, but they are also faster and easier to implement.
Reducing the Space Requirement of Suffix Trees
 Software – Practice and Experience
, 1999
"... We show that suffix trees store various kinds of redundant information. We exploit these redundancies to obtain more space efficient representations. The most space efficient of our representations requires 20 bytes per input character in the worst case, and 10.1 bytes per input character on average ..."
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Cited by 145 (12 self)
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We show that suffix trees store various kinds of redundant information. We exploit these redundancies to obtain more space efficient representations. The most space efficient of our representations requires 20 bytes per input character in the worst case, and 10.1 bytes per input character on average for a collection of 42 files of different type. This is an advantage of more than 8 bytes per input character over previous work. Our representations can be constructed without extra space, and as fast as previous representations. The asymptotic running times of suffix tree applications are retained. Copyright © 1999 John Wiley & Sons, Ltd. KEY WORDS: data structures; suffix trees; implementation techniques; space reduction
The String BTree: A New Data Structure for String Search in External Memory and its Applications.
 Journal of the ACM
, 1998
"... We introduce a new textindexing data structure, the String BTree, that can be seen as a link between some traditional externalmemory and stringmatching data structures. In a short phrase, it is a combination of Btrees and Patricia tries for internalnode indices that is made more effective by a ..."
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Cited by 137 (12 self)
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We introduce a new textindexing data structure, the String BTree, that can be seen as a link between some traditional externalmemory and stringmatching data structures. In a short phrase, it is a combination of Btrees and Patricia tries for internalnode indices that is made more effective by adding extra pointers to speed up search and update operations. Consequently, the String BTree overcomes the theoretical limitations of inverted files, Btrees, prefix Btrees, suffix arrays, compacted tries and suffix trees. String Btrees have the same worstcase performance as Btrees but they manage unboundedlength strings and perform much more powerful search operations such as the ones supported by suffix trees. String Btrees are also effective in main memory (RAM model) because they improve the online suffix tree search on a dynamic set of strings. They also can be successfully applied to database indexing and software duplication.
Fast and Intuitive Clustering of Web Documents
 In Proceedings of the 3rd International Conference on Knowledge Discovery and Data Mining
, 1997
"... Conventional document retrieval systems (e.g., Alta Vista) return long lists of ranked documents in response to user queries. Recently, document clustering has been put forth as an alternative method of organizing retrieval results (Cutting et al. 1992). A person browsing the clusters can discover ..."
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Cited by 114 (2 self)
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Conventional document retrieval systems (e.g., Alta Vista) return long lists of ranked documents in response to user queries. Recently, document clustering has been put forth as an alternative method of organizing retrieval results (Cutting et al. 1992). A person browsing the clusters can discover patterns that could be overlooked in the traditional presentation. This paper describes two novel clustering methods that intersect the documents in a cluster to determine the set of words (or phrases) shared by all the documents in the cluster. We report on experiments that evaluate these intersectionbased clustering methods on collections of snippets returned from Web search engines. First, we show that wordintersection clustering produces superior clusters and does so faster than standard techniques. Second, we show that our O(n log n) time phraseintersection clustering method produces comparable clusters and does so more than two orders of magnitude faster than all methods tested. I...
From Ukkonen to McCreight and Weiner: A Unifying View of LinearTime Suffix Tree Constructions
 ALGORITHMICA
, 1997
"... We review the linear time suffix tree constructions by Weiner, McCreight, and Ukkonen. We use the terminology of the most recent algorithm, Ukkonen's online construction, to explain its historic predecessors. This reveals relationships much closer than one would expect, since the three algorith ..."
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Cited by 86 (7 self)
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We review the linear time suffix tree constructions by Weiner, McCreight, and Ukkonen. We use the terminology of the most recent algorithm, Ukkonen's online construction, to explain its historic predecessors. This reveals relationships much closer than one would expect, since the three algorithms are based on rather different intuitive ideas. Moreover, it completely explains the dierences between these algorithms in terms of simplicity, efficiency, and implementation complexity.
A taxonomy of suffix array construction algorithms
 ACM Computing Surveys
, 2007
"... In 1990, Manber and Myers proposed suffix arrays as a spacesaving 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 abunda ..."
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Cited by 77 (12 self)
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In 1990, Manber and Myers proposed suffix arrays as a spacesaving 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 highlevel 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 ’ worstcase time complexity and use of additional space, together with results of recent experimental test runs on many of their implementations.
Indexing Text using the ZivLempel Trie
 Journal of Discrete Algorithms
, 2002
"... Let a text of u characters over an alphabet of size be compressible to n symbols by the LZ78 or LZW algorithm. We show that it is possible to build a data structure based on the ZivLempel trie that takes 4n log 2 n(1+o(1)) bits of space and reports the R occurrences of a pattern of length m in ..."
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Cited by 69 (44 self)
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Let a text of u characters over an alphabet of size be compressible to n symbols by the LZ78 or LZW algorithm. We show that it is possible to build a data structure based on the ZivLempel trie that takes 4n log 2 n(1+o(1)) bits of space and reports the R occurrences of a pattern of length m in worst case time O(m log(m)+(m+R)log n).