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]

PDF fulltext.pdf - Published Version Restricted to Registered users only Download (247kB) | Request a copy

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
Series.:	Lecture Notes in Computer Science
Publisher:	Springer
Additional Information:	Copyright of this article belongs to Springer.
Department/Centre:	Division of Interdisciplinary Sciences > Supercomputer Education & Research Centre
Date Deposited:	08 Jan 2010 11:51
Last Modified:	19 Sep 2010 04:56
URI:	http://eprints.iisc.ac.in/id/eprint/17331

Actions (login required)

View Item