Suffix arrays: a new method for on-line string searches
SODA '90 Proceedings of the first annual ACM-SIAM symposium on Discrete algorithms
Journal of Algorithms
Improved approximate pattern matching on hypertext
Theoretical Computer Science
Succinct indexable dictionaries with applications to encoding k-ary trees and multisets
SODA '02 Proceedings of the thirteenth 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 data structures for flexible text retrieval systems
Journal of Discrete Algorithms
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
Implicit compression boosting with applications to self-indexing
SPIRE'07 Proceedings of the 14th international conference 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
Computing matching statistics and maximal exact matches on compressed full-text indexes
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
Succincter text indexing with wildcards
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Compressed text indexing with wildcards
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
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Recent advances in nucleic acid sequencing technologies have motivated research into succinct text indexes to represent reference genomes that support efficient pattern matching queries. Similarly, sequencing technologies can also produce reads (patterns) derived from transcripts which need to be aligned to a reference transcriptome. A transcriptome can be modeled as a hypertext-a generalization of a linear text to a graph where nodes contain text and edges denote which nodes can be concatenated. 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 exact 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 common prefixes or when each node has constant degree.