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 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.
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Bedathur, S.J., Haritsa, J.R. (2005). Search-Optimized Suffix-Tree Storage for Biological Applications. In: Bader, D.A., Parashar, M., Sridhar, V., Prasanna, V.K. (eds) High Performance Computing – HiPC 2005. HiPC 2005. Lecture Notes in Computer Science, vol 3769. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11602569_8
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DOI: https://doi.org/10.1007/11602569_8
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