Abstract
To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on straight-line programs and LZ77. In this paper we show how, given a balanced straight-line program for a string S[1..n] whose LZ77 parse consists of z phrases, we can add O(z log log z) words and obtain a compressed self-index for S such that, given a pattern P [1..m], we can list the occ occurrences of P in S in O(m 2 + (m + occ) log log n) time. All previous self-indexes are either larger or slower in the worst case. © 2012 Springer-Verlag.
Cite
CITATION STYLE
Gagie, T., Gawrychowski, P., Kärkkäinen, J., Nekrich, Y., & Puglisi, S. J. (2012). A faster grammar-based self-index. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 7183 LNCS, pp. 240–251). https://doi.org/10.1007/978-3-642-28332-1_21
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