Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Reducing the space requirement of suffix trees
Software—Practice & Experience
Journal of Algorithms
An analysis of the Burrows—Wheeler transform
Journal of the ACM (JACM)
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
High-order entropy-compressed text indexes
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
Proceedings of the 16th Conference on Foundations of Software Technology and Theoretical Computer Science
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
New text indexing functionalities of the compressed suffix arrays
Journal of Algorithms
Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching
SIAM Journal on Computing
Succinct suffix arrays based on run-length encoding
Nordic Journal of Computing
ACM Computing Surveys (CSUR)
A simple optimal representation for balanced parentheses
Theoretical Computer Science
Compressed representations of sequences and full-text indexes
ACM Transactions on Algorithms (TALG)
Compressed Suffix Trees with Full Functionality
Theory of Computing Systems
Space-efficient static trees and graphs
SFCS '89 Proceedings of the 30th Annual Symposium on Foundations of Computer Science
Compressed Text Indexes with Fast Locate
CPM '07 Proceedings of the 18th annual symposium on Combinatorial Pattern Matching
Optimal self-adjusting trees for dynamic string data in secondary storage
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
LATIN'08 Proceedings of the 8th Latin American conference on Theoretical informatics
Engineering the LOUDS succinct tree representation
WEA'06 Proceedings of the 5th international conference on Experimental Algorithms
Suffix trays and suffix trists: structures for faster text indexing
ICALP'06 Proceedings of the 33rd international conference on Automata, Languages and Programming - Volume Part I
A new succinct representation of RMQ-information and improvements in the enhanced suffix array
ESCAPE'07 Proceedings of the First international conference on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies
Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
Storage and Retrieval of Individual Genomes
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Permuted Longest-Common-Prefix Array
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
A Compressed Enhanced Suffix Array Supporting Fast String Matching
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Directly Addressable Variable-Length Codes
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Indexing methods for approximate dictionary searching: Comparative analysis
Journal of Experimental Algorithmics (JEA)
RCSI: scalable similarity search in thousand(s) of genomes
Proceedings of the VLDB Endowment
A Compressed Suffix Tree Based Implementation With Low Peak Memory Usage
Electronic Notes in Theoretical Computer Science (ENTCS)
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Suffix trees are among the most important data structures in stringology, with myriads of applications. Their main problem is space usage, which has triggered much research striving for compressed representations that are still functional. We present a novel compressed suffix tree. Compared to the existing ones, ours is the first achieving at the same time sublogarithmic complexity for the operations, and space usage which goes to zero as the entropy of the text does. Our development contains several novel ideas, such as compressing the longest common prefix information, and totally getting rid of the suffix tree topology, expressing all the suffix tree operations using range minimum queries and a new primitive called next/previous smaller value in a sequence.