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|Title:||Improved approximate string matching using compressed suffix data structures|
|Source:||Lam, T.-W.,Sung, W.-K.,Wong, S.-S. (2005). Improved approximate string matching using compressed suffix data structures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 3827 LNCS : 339-348. ScholarBank@NUS Repository. https://doi.org/10.1007/11602613_35|
|Abstract:||Approximate string matching is about finding a given string pattern in a text by allowing some degree of errors. In this paper we present a space efficient data structure to solve the 1-mismatch and 1-difference problems. Given a text T of length n over a fixed alphabet A, we can preprocess T and give an O(n√log n)-bit space data structure so that, for any query pattern P of length m, we can find all 1-mismatch (or 1-difference) occurrences of P in O(m log log n +occ) time, where occ is the number of occurrences. This is the fastest known query time given that the space of the data structure is o(n log 2 n) bits. The space of our data structure can be further reduced to O(n) if we can afford a slow down factor of log εn, for 0 < ε ≤ 1. Furthermore, our solution can be generalized to solve the k-mismatch (and the k-difference) problem in O(|A| km k(k + log log n) + occ) and O(log ε n(|A| km k(k + log log n) + occ)) query time using an O(n√log n)-bit and an O(n)-bit indexing data structures, respectively. © Springer-Verlag Berlin Heidelberg 2005.|
|Source Title:||Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|
|Appears in Collections:||Staff Publications|
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