Tree pattern matching and subset matching in deterministic O(n log3 n)-time
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
Efficient string matching: an aid to bibliographic search
Communications of the ACM
Approximate subset matching with Don't Cares
SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
Designing seeds for similarity search in genomic DNA
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
FLASH: A Fast Look-Up Algorithm for String Homology
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
Better filtering with gapped q-grams
Fundamenta Informaticae - Special issue on computing patterns in strings
On spaced seeds for similarity search
Discrete Applied Mathematics
Vector seeds: An extension to spaced seeds
Journal of Computer and System Sciences - Special issue on bioinformatics II
Indel seeds for homology search
Bioinformatics
Fast pattern-matching on indeterminate strings
Journal of Discrete Algorithms
Optimal probing patterns for sequencing by hybridization
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Rapid homology search with two-stage extension and daughter seeds
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
Masking patterns in sequences: A new class of motif discovery with don't cares
Theoretical Computer Science
Seed design framework for mapping SOLiD reads
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
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We study the pattern matching automaton introduced in [1] for the purpose of seed-based similarity search. We show that our definition provides a compact automaton, much smaller than the one obtained by applying the Aho-Corasick construction. We study properties of this automaton and present an efficient implementation of the automaton construction. We also present some experimental results and show that this automaton can be successfully applied to more general situations.