Fast Label Extraction in the CDAWG
Abstract
The compact directed acyclic word graph (CDAWG) of a string of length takes space proportional just to the number of right extensions of the maximal repeats of , and it is thus an appealing index for highly repetitive datasets, like collections of genomes from similar species, in which grows significantly more slowly than . We reduce from to the time needed to count the number of occurrences of a pattern of length , using an existing data structure that takes an amount of space proportional to the size of the CDAWG. This implies a reduction from to in the time needed to locate all the occurrences of the pattern. We also reduce from to the time needed to read the characters of the label of an edge of the suffix tree of , and we reduce from to the time needed to compute the matching statistics between a query of length and , using an existing representation of the suffix tree based on the CDAWG. All such improvements derive from extracting the label of a vertex or of an arc of the CDAWG using a straight-line program induced by the reversed CDAWG.
Cite
@article{arxiv.1707.08197,
title = {Fast Label Extraction in the CDAWG},
author = {Djamal Belazzougui and Fabio Cunial},
journal= {arXiv preprint arXiv:1707.08197},
year = {2017}
}
Comments
16 pages, 1 figure. In proceedings of the 24th International Symposium on String Processing and Information Retrieval (SPIRE 2017). arXiv admin note: text overlap with arXiv:1705.08640