PATRICIA—Practical Algorithm To Retrieve Information Coded in Alphanumeric
Journal of the ACM (JACM)
High-order entropy-compressed text indexes
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
Scaling and related techniques for geometry problems
STOC '84 Proceedings of the sixteenth annual ACM symposium on Theory of computing
Application of Lempel--Ziv factorization to the approximation of grammar-based compression
Theoretical Computer Science
Journal of the ACM (JACM)
ACM Computing Surveys (CSUR)
Preserving order in a forest in less than logarithmic time
SFCS '75 Proceedings of the 16th Annual Symposium on Foundations of Computer Science
Geometric Burrows-Wheeler Transform: Linking Range Searching and Text Indexing
DCC '08 Proceedings of the Data Compression Conference
Self-indexed Text Compression Using Straight-Line Programs
MFCS '09 Proceedings of the 34th International Symposium on Mathematical Foundations of Computer Science 2009
On Entropy-Compressed Text Indexing in External Memory
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Information Processing Letters
Indexing similar DNA sequences
AAIM'10 Proceedings of the 6th international conference on Algorithmic aspects in information and management
Relative Lempel-Ziv compression of genomes for large-scale storage and retrieval
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
Note: Combined data structure for previous- and next-smaller-values
Theoretical Computer Science
Orthogonal range searching on the RAM, revisited
Proceedings of the twenty-seventh annual symposium on Computational geometry
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
ESP-index: a compressed index based on edit-sensitive parsing
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
IEEE Transactions on Information Theory
Fast relative lempel-ziv self-index for similar sequences
FAW-AAIM'12 Proceedings of the 6th international Frontiers in Algorithmics, and Proceedings of the 8th international conference on Algorithmic Aspects in Information and Management
Improved grammar-based compressed indexes
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
ESP-index: A compressed index based on edit-sensitive parsing
Journal of Discrete Algorithms
RCSI: scalable similarity search in thousand(s) of genomes
Proceedings of the VLDB Endowment
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To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on straight-line programs and LZ77. In this paper we show how, given a balanced straight-line program for a string S[1..n] whose LZ77 parse consists of z phrases, we can add O(z log log z) words and obtain a compressed self-index for S such that, given a pattern P [1..m], we can list the occ occurrences of P in S in O(m2 + (m + occ) log log n) time. All previous self-indexes are either larger or slower in the worst case.