On-line pattern matching on similar texts

Roberto P Grossi (1, 2) , Costas S Iliopoulos (3) , Chang Liu (3) , Nadia P Pisanti (1, 2) , Solon P Pissis (3) , Ahmad Retha (3) , Giovanna Rosone (4, 1) , Fatima Vayani (3) , Luca P Versari (1)

1 DI - Dipartimento di Informatica [Pisa]
2 ERABLE - Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale
3 Department of Informatics [King's College London]
4 Università degli studi di Palermo - University of Palermo

Pattern matching on a set of similar texts has received much attention, especially recently, mainly due to its application in cataloguing human genetic variation. In particular, many different algorithms have been proposed for the off-line version of this problem; that is, constructing a compressed index for a set of similar texts in order to answer pattern matching queries efficiently. However, the on-line, more fundamental, version of this problem is a rather undeveloped topic. Solutions to the on-line version can be beneficial for a number of reasons; for instance, efficient on-line solutions can be used in combination with partial indexes as practical trade-offs. We make here an attempt to close this gap via proposing two efficient algorithms for this problem. Notably, one of the algorithms requires time linear in the size of the texts' representation, for short patterns. Furthermore, experimental results confirm our theoretical findings in practical terms.

Mots clés: string algorithms; pattern matching; degenerate strings; elastic-degenerate; strings; on-line algorithms

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

Roberto P Grossi, Costas S Iliopoulos, Chang Liu, Nadia P Pisanti, Solon P Pissis, et al.. On-line pattern matching on similar texts. 28th Annual Symposium on Combinatorial Pattern Matching (CPM'17), 2017, Varsovie, Poland. pp.7 - 8, ⟨10.4230/LIPIcs.CPM.2017.07⟩. ⟨hal-01526650⟩