### Abstract

This paper deals with the approximate string-matching problem with Hamming distance. The approximate string-matching with k-mismatches problem is to find all locations at which a query of length m matches a factor of a text of length n with k or fewer mismatches. The approximate string-matching algorithms have both pleasing theoretical features, as well as direct applications, especially in computational biology.We consider a generalisation of this problem, the fixed-length approximate string-matching with k-mismatches problem: given a text t, a pattern x and an integer ℓ, search for all the occurrences in t of all factors of x of length ℓ with k or fewer mismatches with a factor of t. We present a practical parallel algorithm of comparable simplicity that requires only O(nm[ℓ/w]/p) time, where w is the word size of the machine (e.g. 32 or 64 in practice) and p the number of processors. Thus the algorithm's performance is independent of k and the alphabet size |Σ|. The proposed parallel algorithm makes use ofmessage-passing parallelism model, and word-level parallelism for efficient approximate string-matching.

Original language | English |
---|---|

Title of host publication | Algorithms and Applications - Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday |

Editors | Tapio Elomaa, Heikki Mannila, Pekka Orponen |

Pages | 92-101 |

Number of pages | 10 |

DOIs | |

Publication status | Published - 28 Dec 2010 |

Externally published | Yes |

### Publication series

Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
---|---|

Volume | 6060 LNCS |

ISSN (Print) | 0302-9743 |

ISSN (Electronic) | 1611-3349 |

### Keywords

- Approximate stringmatching
- Parallel algorithms
- String algorithms

## Fingerprint Dive into the research topics of 'A parallel algorithm for fixed-length approximate string-matching with k-mismatches'. Together they form a unique fingerprint.

## Cite this

*Algorithms and Applications - Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday*(pp. 92-101). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6060 LNCS). https://doi.org/10.1007/978-3-642-12476-1_6