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ICDE
2004
IEEE

Engineering a Fast Online Persistent Suffix Tree Construction

12 years 11 months ago
Engineering a Fast Online Persistent Suffix Tree Construction
Online persistent suffix tree construction has been considered impractical due to its excessive I/O costs. However, these prior studies have not taken into account the effects of the buffer management policy and the internal node structure of the suffix tree on I/O behavior of construction and subsequent retrievals over the tree. In this paper, we study these two issues in detail in the context of large genomic DNA and Protein sequences. In particular, we make the following contributions: (i) a novel, low-overhead buffering policy called TOP-Q which improves the on-disk behavior of suffix tree construction and subsequent retrievals, and (ii) empirical evidence that the space efficient linked-list representation of suffix tree nodes provides significantly inferior performance when compared to the array representation. These results demonstrate that a careful choice of implementation strategies can make online persistent suffix tree construction considerably more scalable ? in terms of ...
Srikanta J. Bedathur, Jayant R. Haritsa
Added 01 Nov 2009
Updated 01 Nov 2009
Type Conference
Year 2004
Where ICDE
Authors Srikanta J. Bedathur, Jayant R. Haritsa
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