Database indexing for large DNA and protein sequence collections
The VLDB Journal — The International Journal on Very Large Data Bases
Towards Automatic Clustering of Protein Sequences
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Distributed suffix trees and their application to large-scale genomic analysis
ICCMSE '03 Proceedings of the international conference on Computational methods in sciences and engineering
Periscope/SQ: interactive exploration of biological sequence databases
VLDB '07 Proceedings of the 33rd international conference on Very large data bases
Fast profile matching algorithms – A survey
Theoretical Computer Science
Distributed and paged suffix trees for large genetic databases
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Fast search algorithms for position specific scoring matrices
BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
Finding Significant Matches of Position Weight Matrices in Linear Time
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Parallel Position Weight Matrices algorithms
Parallel Computing
On-Line linear-time construction of word suffix trees
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Protein structure abstractionand automatic clustering using secondary structure element sequences
ICCSA'05 Proceedings of the 2005 international conference on Computational Science and Its Applications - Volume Part II
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