Journal of Algorithms
Improved approximate pattern matching on hypertext
Theoretical Computer Science
High-order entropy-compressed text indexes
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
A Linear Time Pattern Matching Algorithm Between a String and a Tree
CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
Opportunistic data structures with applications
FOCS '00 Proceedings of the 41st Annual Symposium on Foundations of Computer Science
ACM Computing Surveys (CSUR)
Succinct Representations of Arbitrary Graphs
ESA '08 Proceedings of the 16th annual European symposium on Algorithms
Succinct Orthogonal Range Search Structures on a Grid with Applications to Text Indexing
WADS '09 Proceedings of the 11th International Symposium on Algorithms and Data Structures
Self-indexed Text Compression Using Straight-Line Programs
MFCS '09 Proceedings of the 34th International Symposium on Mathematical Foundations of Computer Science 2009
Succinct Text Indexing with Wildcards
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Space efficient indexes for string matching with don't cares
ISAAC'07 Proceedings of the 18th international conference on Algorithms and computation
Succincter text indexing with wildcards
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Compact rich-functional binary relation representations
LATIN'10 Proceedings of the 9th Latin American conference on Theoretical Informatics
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Recent advances in nucleic acid sequencing technology has motivated research into succinct text indexes to represent reference genomes that support efficient pattern matching queries. Similar sequencing technology can also produce millions of reads (patterns) derived from transcripts which need to be aligned to a reference transcriptome. A transcriptome can be modeled as a hypertext. Motivated by this application, we propose the first succinct index for hypertext. The index can model any hypertext and places no restriction on the graph topology. We also propose a new pattern matching algorithm, capable of aligning a pattern to any path in the hypertext, that is especially efficient when few nodes of the hypertext share the same text--in this important case, our algorithm is a significant improvement over all existing approaches.