Algorithms 2013, 6(2), 319-351; doi:10.3390/a6020319
Article

Practical Compressed Suffix Trees

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Received: 18 March 2013; in revised form: 24 April 2013 / Accepted: 26 April 2013 / Published: 21 May 2013
(This article belongs to the Special Issue Algorithms for Sequence Analysis and Storage)
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Abstract: The suffix tree is an extremely important data structure in bioinformatics. Classical implementations require much space, which renders them useless to handle large sequence collections. Recent research has obtained various compressed representations for suffix trees, with widely different space-time tradeoffs. In this paper we show how the use of range min-max trees yields novel representations achieving practical space/time tradeoffs. In addition, we show how those trees can be modified to index highly repetitive collections, obtaining the first compressed suffix tree representation that effectively adapts to that scenario.
Keywords: suffix trees; compressed data structures; repetitive sequence collections; bioinformatics
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Abeliuk, A.; Cánovas, R.; Navarro, G. Practical Compressed Suffix Trees. Algorithms 2013, 6, 319-351.

AMA Style

Abeliuk A, Cánovas R, Navarro G. Practical Compressed Suffix Trees. Algorithms. 2013; 6(2):319-351.

Chicago/Turabian Style

Abeliuk, Andrés; Cánovas, Rodrigo; Navarro, Gonzalo. 2013. "Practical Compressed Suffix Trees." Algorithms 6, no. 2: 319-351.

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