Years and Authors of Summarized Original Work
2007; Sadakane
2009; Fischer, Mäkinen, Navarro
2010; Ohlebusch, Fischer, Gog
2011; Russo, Navarro, Oliveira
Problem Definition
The problem consists in representing suffix trees in main memory. The representation needs to support operations efficiently, using a reasonable amount of space.
Suffix trees were proposed by Weiner in 1973 [16]. Donald Knuth called them the “Algorithm of the Year.” Their ubiquitous nature was quickly perceived and used to solve a myriad of string processing problems. The downside of this flexibility was the notorious amount of space necessary to keep it in main memory. A direct implementation is several times larger than the file it is indexing. Initial research into this matter discovered smaller data structures, sometimes by sacrificing functionality, namely, suffix arrays [6], directed acyclic word graphs [5], or engineered solutions.
Suffix tree of string abbbab, with the leaves...
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Recommended Reading
Abeliuk A, Cánovas R, Navarro G (2013) Practical compressed suffix trees. Algorithms 6(2):319–351
Abouelhoda MI, Kurtz S, Ohlebusch E (2004) Replacing suffix trees with enhanced suffix arrays. J Discr Algorithms 2(1):53–86
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Fischer J, Mäkinen V, Navarro G (2009) Faster entropy-bounded compressed suffix trees. Theor Comput Sci 410(51):5354–5364
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Navarro G, Russo L (2014) Fast fully-compressed suffix trees. In: Proceedings of the 24th data compression conference (DCC), Snowbird, pp 283–291
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Russo L, Navarro G, Oliveira A (2011) Fully-compressed suffix trees. ACM Trans Algorithms (TALG) 7(4):article 53, 35p
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Weiner P (1973) Linear pattern matching algorithms. In: IEEE conference record of 14th annual symposium on switching and automata theory, 1973. SWAT’08. IEEE, pp 1–11. http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=4569717
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Russo, L.M.S. (2016). Compressed Suffix Trees. In: Kao, MY. (eds) Encyclopedia of Algorithms. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2864-4_643
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