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Published in:
2005 | OriginalPaper | Chapter
Search-Optimized Suffix-Tree Storage for Biological Applications
Authors : Srikanta J. Bedathur, Jayant R. Haritsa
Published in: High Performance Computing – HiPC 2005
Publisher: Springer Berlin Heidelberg
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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 sequencesearch 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.