Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
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
LATIN '00 Proceedings of the 4th Latin American Symposium on Theoretical Informatics
Succinct ordinal trees with level-ancestor queries
SODA '04 Proceedings of the fifteenth annual ACM-SIAM symposium on Discrete algorithms
New text indexing functionalities of the compressed suffix arrays
Journal of Algorithms
The level ancestor problem simplified
Theoretical Computer Science - Latin American theorotical informatics
When indexing equals compression: Experiments with compressing suffix arrays and applications
ACM Transactions on Algorithms (TALG)
ACM Computing Surveys (CSUR)
Compressed representations of sequences and full-text indexes
ACM Transactions on Algorithms (TALG)
Compressed Suffix Trees with Full Functionality
Theory of Computing Systems
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
Dynamic rank-select structures with applications to run-length encoded texts
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
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
An(other) Entropy-Bounded Compressed Suffix Tree
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Dynamic Fully-Compressed Suffix Trees
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Indexed Hierarchical Approximate String Matching
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
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
Faster entropy-bounded compressed suffix trees
Theoretical Computer Science
Dynamic extended suffix arrays
Journal of Discrete Algorithms
Information Processing Letters
Sampled longest common prefix array
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
Parallel and distributed compressed indexes
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
Indexing methods for approximate dictionary searching: Comparative analysis
Journal of Experimental Algorithmics (JEA)
Note: Combined data structure for previous- and next-smaller-values
Theoretical Computer Science
Representing a bilingual lexicon with suffix trees
Proceedings of the 2011 ACM Symposium on Applied Computing
ACM Transactions on Algorithms (TALG)
Inverted indexes for phrases and strings
Proceedings of the 34th international ACM SIGIR conference on Research and development in Information Retrieval
Practical compressed suffix trees
SEA'10 Proceedings of the 9th international conference on Experimental Algorithms
On compressing and indexing repetitive sequences
Theoretical Computer Science
Hi-index | 0.00 |
Suffix trees are by far the most important data structure in stringology, with myriads of applications in fields like bioinformatics and information retrieval. Classical representations of suffix trees require O(n log n) bits of space, for a string of size n. This is considerably more than the n log2 σ bits needed for the string itself, where σ is the alphabet size. The size of suffix trees has been a barrier to their wider adoption in practice. Recent compressed suffix tree representations require just the space of the compressed string plus Θ(n) extra bits. This is already spectacular, but still unsatisfactory when σ is small as in DNA sequences. In this paper we introduce the first compressed suffix tree representation that breaks this linear-space barrier. Our representation requires sublinear extra space and supports a large set of navigational operations in logarithmic time. An essential ingredient of our representation is the lowest common ancestor (LCA) query. We reveal important connections between LCA queries and suffix tree navigation.