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-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.
| Original language | English |
|---|---|
| Title of host publication | Frontiers in Algorithmics - 8th International Workshop, FAW 2014, Proceedings |
| Publisher | Springer Verlag |
| Pages | 141-150 |
| Number of pages | 10 |
| ISBN (Print) | 9783319080154 |
| DOIs | |
| Publication status | Published - 2014 |
| Event | 8th International Frontiers of Algorithmics Workshop, FAW 2014 - Zhangjiajie, China Duration: 2014 Jun 28 → 2014 Jun 30 |
Publication series
| Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
|---|---|
| Volume | 8497 LNCS |
| ISSN (Print) | 0302-9743 |
| ISSN (Electronic) | 1611-3349 |
Other
| Other | 8th International Frontiers of Algorithmics Workshop, FAW 2014 |
|---|---|
| Country/Territory | China |
| City | Zhangjiajie |
| Period | 14/6/28 → 14/6/30 |
Bibliographical note
Funding Information:This research was supported by the Basic Science Research Program through NRF funded by MEST (2012R1A1A2044562).
Funding Information:
Kim was supported by NRF (National Research Foundation of Korea) Grant funded by the Korean Government (NRF-2013-Global Ph.D. Fellowship Program).
All Science Journal Classification (ASJC) codes
- Theoretical Computer Science
- Computer Science(all)