An inversion is one of the important operations in bio sequence analysis and the sequence alignment problem is well-studied for efficient bio sequence comparisons. We investigate the string matching problem allowing inversions: Given a pattern P and a text T, find all indices of matching substrings of T when non-overlapping inversions are allowed. We design an O(nm) algorithm using O(m) space, where n is the size of T and m is the size of P. The proposed algorithm improves the space complexity of the best-known algorithm, which runs in O(nm) time with O(m 2) space. We, furthermore, improve the algorithm and achieve O(max{n, min{nm,nm 5-t/2 }}) average runtime for an alphabet of size t, which is faster than O(nm) when t ≥ 4. © 2014 Springer International Publishing.
CITATION STYLE
Kim, H., & Han, Y. S. (2014). Space-efficient approximate string matching allowing inversions in fast average time. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8497 LNCS, pp. 141–150). Springer Verlag. https://doi.org/10.1007/978-3-319-08016-1_13
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