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 \(\mathcal{O}{z log log z}\) 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 \(\mathcal{O}({m^{2} + (m + occ) log log n})\) time. All previous self-indexes are either larger or slower in the worst case.
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Gagie, T., Gawrychowski, P., Kärkkäinen, J., Nekrich, Y., Puglisi, S.J. (2012). A Faster Grammar-Based Self-index. In: Dediu, AH., Martín-Vide, C. (eds) Language and Automata Theory and Applications. LATA 2012. Lecture Notes in Computer Science, vol 7183. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28332-1_21
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DOI: https://doi.org/10.1007/978-3-642-28332-1_21
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