In-place update of suffix array while recoding words

Matthias Gallé 1, * Pierre Peterlongo 1 François Coste 1
* Corresponding author
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : Motivated by grammatical inference and data compression applications, we propose an algorithm to update a suffix array while in the indexed text some occurrences of a given word are substituted by a new character. Compared to other published index update methods, the problem addressed here may require the modification of a large number of distinct positions over the original text. The proposed algorithm uses the specific internal order of suffix arrays in order to update simultaneously groups of indices, and ensures that only indices to be modified are visited. Experiments confirm a significant execution time speed-up compared to the construction of suffix array from scratch at each step of the application.
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Matthias Gallé, Pierre Peterlongo, François Coste. In-place update of suffix array while recoding words. International Journal of Foundations of Computer Science, World Scientific Publishing, 2009, 20 (6), pp.1025-1045. ⟨10.1142/S0129054109007029⟩. ⟨inria-00471599⟩

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