Abstract
To store and search genomic databases efficiently, researchers have recently started building self-indexes based on LZ77. As the name suggests, a self-index for a string supports both random access and pattern matching queries. In this paper we show how, given a string S [1..n] whose LZ77 parse consists of z phrases, we can store a self-index for S in \(\mathcal{O}({z \log (n / z)})\) space such that later, first, given a position i and a length ℓ, we can extract S [i..i + ℓ − 1] in \(\mathcal{O}({\ell + \log n})\) time; second, given a pattern P [1..m], we can list the occ occurrences of P in S in \(\mathcal{O}({m \log m + occ \log \log n})\) time.
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Gagie, T., Gawrychowski, P., Kärkkäinen, J., Nekrich, Y., Puglisi, S.J. (2014). LZ77-Based Self-indexing with Faster Pattern Matching. In: Pardo, A., Viola, A. (eds) LATIN 2014: Theoretical Informatics. LATIN 2014. Lecture Notes in Computer Science, vol 8392. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-54423-1_63
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DOI: https://doi.org/10.1007/978-3-642-54423-1_63
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