Filtering search: a new approach to query answering
SIAM Journal on Computing
An efficient representation for sparse sets
ACM Letters on Programming Languages and Systems (LOPLAS)
STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing
Efficient string matching: an aid to bibliographic search
Communications of the ACM
Opportunistic data structures with applications
FOCS '00 Proceedings of the 41st Annual Symposium on Foundations of Computer Science
STRING-MATCHING AND OTHER PRODUCTS
STRING-MATCHING AND OTHER PRODUCTS
Dictionary matching and indexing with errors and don't cares
STOC '04 Proceedings of the thirty-sixth annual ACM symposium on Theory of computing
ACM Computing Surveys (CSUR)
Compressed indexes for dynamic text collections
ACM Transactions on Algorithms (TALG)
Compressed Index for Dictionary Matching
DCC '08 Proceedings of the Data Compression Conference
Orthogonal range searching in linear and almost-linear space
Computational Geometry: Theory and Applications
Space efficient indexes for string matching with don't cares
ISAAC'07 Proceedings of the 18th international conference on Algorithms and computation
Succinct dictionary matching with no slowdown
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Compression, indexing, and retrieval for massive string data
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Faster compressed dictionary matching
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
Worst case efficient single and multiple string matching in the RAM model
IWOCA'10 Proceedings of the 21st international conference on Combinatorial algorithms
Succincter text indexing with wildcards
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
A succinct index for hypertext
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
Compressed text indexing with wildcards
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
An index structure for spaced seed search
ISAAC'11 Proceedings of the 22nd international conference on Algorithms and Computation
Worst-case efficient single and multiple string matching on packed texts in the word-RAM model
Journal of Discrete Algorithms
String indexing for patterns with wildcards
SWAT'12 Proceedings of the 13th Scandinavian conference on Algorithm Theory
Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samples
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Journal of Discrete Algorithms
Faster compressed dictionary matching
Theoretical Computer Science
Compressed text indexing with wildcards
Journal of Discrete Algorithms
Compressed indexes for text with wildcards
Theoretical Computer Science
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A succinct text index uses space proportional to the text itself, say, two times n log*** for a text of n characters over an alphabet of size *** . In the past few years, there were several exciting results leading to succinct indexes that support efficient pattern matching. In this paper we present the first succinct index for a text that contains wildcards. The space complexity of our index is (3 + o (1))n log*** + O (***logn ) bits, where *** is the number of wildcard groups in the text. Such an index finds applications in indexing genomic sequences that contain single-nucleotide polymorphisms (SNP), which could be modeled as wildcards. In the course of deriving the above result, we also obtain an alternate succinct index of a set of d patterns for the purpose of dictionary matching. When compared with the succinct index in the literature, the new index doubles the size (precisely, from n log*** to 2 n log*** , where n is the total length of all patterns), yet it reduces the matching time to O (m log*** + m logd + occ ), where m is the length of the query text. It is worth-mentioning that the time complexity no longer depends on the total dictionary size.