Blocking for external graph searching
PODS '93 Proceedings of the twelfth ACM SIGACT-SIGMOD-SIGART symposium on Principles of database systems
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
Journal of Algorithms
Database indexing for large DNA and protein sequence collections
The VLDB Journal — The International Journal on Very Large Data Bases
A Database Index to Large Biological Sequences
Proceedings of the 27th International Conference on Very Large Data Bases
Clustering Techniques for Minimizing External Path Length
VLDB '96 Proceedings of the 22th International Conference on Very Large Data Bases
Approximate String-Matching over Suffix Trees
CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
Suffix Trees (and Relatives) Come of Age in Bioinformatics
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Engineering a Fast Online Persistent Suffix Tree Construction
ICDE '04 Proceedings of the 20th International Conference on Data Engineering
Practical suffix tree construction
VLDB '04 Proceedings of the Thirtieth international conference on Very large data bases - Volume 30
Approximate string matching in sublinear expected time
SFCS '90 Proceedings of the 31st Annual Symposium on Foundations of Computer Science
Genome-scale disk-based suffix tree indexing
Proceedings of the 2007 ACM SIGMOD international conference on Management of data
Storing semi-structured data on disk drives
ACM Transactions on Storage (TOS)
Serial and parallel methods for i/o efficient suffix tree construction
Proceedings of the 2009 ACM SIGMOD International Conference on Management of data
Optimal self-adjusting trees for dynamic string data in secondary storage
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
I/O efficient algorithms for serial and parallel suffix tree construction
ACM Transactions on Database Systems (TODS)
Toward optimal disk layout of genome scale suffix trees
SEAL'10 Proceedings of the 8th international conference on Simulated evolution and learning
Obtaining provably good performance from suffix trees in secondary storage
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
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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.