### 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 |
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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 Jan 1 |

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) |
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Volume | 8497 LNCS |

ISSN (Print) | 0302-9743 |

ISSN (Electronic) | 1611-3349 |

### Other

Other | 8th International Frontiers of Algorithmics Workshop, FAW 2014 |
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Country | China |

City | Zhangjiajie |

Period | 14/6/28 → 14/6/30 |

### Fingerprint

### All Science Journal Classification (ASJC) codes

- Theoretical Computer Science
- Computer Science(all)

### Cite this

*Frontiers in Algorithmics - 8th International Workshop, FAW 2014, Proceedings*(pp. 141-150). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8497 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-08016-1_13