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Conference Paper

Search-Optimized Suffix-Tree Storage for Biological Applications


Bedathur,  Srikanta
Databases and Information Systems, MPI for Informatics, Max Planck Society;

Haritsa,  Jayant
Max Planck Society;

Varadarajan,  Sridhar
Max Planck Society;

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Bedathur, S., & Haritsa, J. (2006). Search-Optimized Suffix-Tree Storage for Biological Applications. In 12th IEEE International Conference on High Performance Computing (HiPC) (pp. 29-39). Berlin, Germany: Springer.

Cite as: https://hdl.handle.net/11858/00-001M-0000-000F-23E8-A
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.