Longest repeated motif with a block of don't cares

Maxime Crochemore (1, 2) , Costas S. Iliopoulos (2) , Manal Mohamed (2) , Marie-France Sagot (3)

1 LIGM - Laboratoire d'Informatique Gaspard-Monge
2 Department of Computer Science [London]
3 Baobab

We introduce an algorithm for extracting all longest repeats with k don’t cares from a given sequence. Such repeats are composed of two parts separated by a block of k don’t care symbols. The algorithm uses suffix trees to fulfill this task and relies on the ability to answer the lowest common ancestor queries in constant time. It requires O(n log n) time in the worst-case.

Domaines: Algorithme et structure de données [cs.DS]

Maxime Crochemore, Costas S. Iliopoulos, Manal Mohamed, Marie-France Sagot. Longest repeated motif with a block of don't cares. 6th Latin American Theoretical Informatics (LATIN'04), 2004, Buenos Aires, Argentina. pp.271-278, ⟨10.1007/978-3-540-24698-5_31⟩. ⟨hal-00619983⟩