Using minimal absent words to build phylogeny

Supaporn Chairungsee (1) , Maxime Crochemore (1, 2)

1 Informatics
2 LIGM - Laboratoire d'Informatique Gaspard-Monge

An absent word in a sequence is a segment that does not occur in the given sequence. It is a minimal absent word if all its proper factors occur in the given sequence. In this paper, we review the concept of minimal absent words, which includes the notion of shortest absent word. We present an efficient method for computing the minimal absent words of bounded length using a trie of bounded depth, representing bounded length factors. This method produces the minimal absent words of given bounded length, and furthermore our technique provides a linear-time algorithm with less memory usage than previous solutions. We also present an approach, the length-weighted index, to distinguish sequences of different organisms using their minimal absent words. The results show that we can build a phylogenetic tree based on the information collected.

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

Supaporn Chairungsee, Maxime Crochemore. Using minimal absent words to build phylogeny. Theoretical Computer Science, 2012, 450, pp.109-116. ⟨10.1016/j.tcs.2012.04.031⟩. ⟨hal-00742560⟩