TY - GEN
T1 - Space-efficient approximate string matching allowing inversions in fast average time
AU - Kim, Hwee
AU - Han, Yo Sub
N1 - Copyright:
Copyright 2014 Elsevier B.V., All rights reserved.
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84903600987&partnerID=8YFLogxK
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U2 - 10.1007/978-3-319-08016-1_13
DO - 10.1007/978-3-319-08016-1_13
M3 - Conference contribution
AN - SCOPUS:84903600987
SN - 9783319080154
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 141
EP - 150
BT - Frontiers in Algorithmics - 8th International Workshop, FAW 2014, Proceedings
PB - Springer Verlag
T2 - 8th International Frontiers of Algorithmics Workshop, FAW 2014
Y2 - 28 June 2014 through 30 June 2014
ER -