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  Search-Optimized Suffix-Tree Storage for Biological Applications

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.

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Item Permalink: https://hdl.handle.net/11858/00-001M-0000-000F-23E8-A Version Permalink: https://hdl.handle.net/11858/00-001M-0000-000F-23EA-6
Genre: Conference Paper

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 Creators:
Bedathur, Srikanta1, Author           
Haritsa, Jayant2, Author
Bader, David A., Editor
Parashar, Manish, Editor
Varadarajan, Sridhar2, Editor
Prasanna, Viktor K., Editor
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1Databases and Information Systems, MPI for Informatics, Max Planck Society, ou_24018              
2Max Planck Society, ou_persistent13              

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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.

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Language(s): eng - English
 Dates: 2007-04-272006
 Publication Status: Issued
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 Identifiers: eDoc: 314538
Other: Local-ID: C1256DBF005F876D-87F8945181612E4FC125728A003BC3ED-Bedathur2005
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Title: Untitled Event
Place of Event: Goa, India
Start-/End Date: 2005-12-18

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Title: 12th IEEE International Conference on High Performance Computing (HiPC)
Source Genre: Proceedings
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Publ. Info: Berlin, Germany : Springer
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: 29 - 39 Identifier: ISBN: 978-3-540-30936-9

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Title: Lecture Notes in Computer Science
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Pages: - Volume / Issue: 3769 Sequence Number: - Start / End Page: - Identifier: -