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Search-Optimized Suffix-Tree Storage for Biological Applications

Bedathur, Srikanta J and Haritsa, Jayant R (2005) Search-Optimized Suffix-Tree Storage for Biological Applications. [Book Chapter]

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Abstract

Suffix-trees are popular indexing structures for various sequence processing problems in biological data management. We investigate here the possibility of enhancing the search efficiency of disk-resident suffix-trees through customized layouts of tree-nodes to disk-pages. Specifically, we propose a new layout strategy, called Stellar, that provides significantly improved search performance on a representative set of real genomic sequences. Further, Stellar supports both the standard root-to-leaf lookup queries as well as sophisticated sequence-search algorithms that exploit the suffix-links of suffix-trees. Our results are encouraging with regard to the ultimate objective of seamlessly integrating sequence processing in database engines.

Item Type: Book Chapter
Additional Information: Copyright of this article belongs to Springer.
Department/Centre: Division of Information Sciences > Supercomputer Education & Research Centre
Date Deposited: 08 Jan 2010 11:51
Last Modified: 19 Sep 2010 04:56
URI: http://eprints.iisc.ernet.in/id/eprint/17331

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