Abstract
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-overlap** 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 \(\displaystyle O(\max\{n,\min\{nm, nm^{\frac{5-t}{2}}\}\})\) average runtime for an alphabet of size t, which is faster than O(nm) when t ≥ 4.
This research was supported by the Basic Science Research Program through NRF funded by MEST (2012R1A1A2044562).
Kim was supported by NRF (National Research Foundation of Korea) Grant funded by the Korean Government (NRF-2013-Global Ph.D. Fellowship Program).
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Kim, H., Han, YS. (2014). Space-Efficient Approximate String Matching Allowing Inversions in Fast Average Time. In: Chen, J., Hopcroft, J.E., Wang, J. (eds) Frontiers in Algorithmics. FAW 2014. Lecture Notes in Computer Science, vol 8497. Springer, Cham. https://doi.org/10.1007/978-3-319-08016-1_13
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DOI: https://doi.org/10.1007/978-3-319-08016-1_13
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