The Gapped-Factor Tree

Pierre Peterlongo (1) , Julien Allali (1) , Marie-France Sagot (2, 3, 4)

1 LIGM - Laboratoire d'Informatique Gaspard-Monge
2 HELIX - Computer science and genomics
3 DCS - Department of Computer Science
4 Baobab

We present a data structure to index a specific kind of factors, that is of substrings, called gapped-factors. A gapped-factor is a factor containing a gap that is ignored during the indexation. The data structure presented is based on the suffix tree and indexes all the gapped-factors of a text with a fixed size of gap, and only those. The construction of this data structure is done online in linear time and space. Such a data structure may play an important role in various pattern matching and motif inference problems, for instance in text filtration.

Domaines: Autre [cs.OH]

Pierre Peterlongo, Julien Allali, Marie-France Sagot. The Gapped-Factor Tree. Prague Stringology Conference 2006, 2006, Prague, Czech Republic. pp.182--196. ⟨hal-00306572⟩