Efficient algorithms for document retrieval problems
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
Application of Lempel--Ziv factorization to the approximation of grammar-based compression
Theoretical Computer Science
Compression boosting in optimal linear time using the Burrows-Wheeler Transform
SODA '04 Proceedings of the fifteenth annual ACM-SIAM symposium on Discrete algorithms
Journal of the ACM (JACM)
Rank/select operations on large alphabets: a tool for text indexing
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
A Simple Statistical Algorithm for Biological Sequence Compression
DCC '07 Proceedings of the 2007 Data Compression Conference
FOCS '08 Proceedings of the 2008 49th Annual IEEE Symposium on Foundations of Computer Science
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
Orthogonal range searching in linear and almost-linear space
Computational Geometry: Theory and Applications
Human genomes as email attachments
Bioinformatics
Self-indexed Text Compression Using Straight-Line Programs
MFCS '09 Proceedings of the 34th International Symposium on Mathematical Foundations of Computer Science 2009
Implicit compression boosting with applications to self-indexing
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
LZ77-Like Compression with Fast Random Access
DCC '10 Proceedings of the 2010 Data Compression Conference
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
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
Reference sequence construction for relative compression of genomes
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
Random access to grammar-compressed strings
Proceedings of the twenty-second annual ACM-SIAM symposium on Discrete Algorithms
A faster grammar-based self-index
LATA'12 Proceedings of the 6th international conference on Language and Automata Theory and Applications
A universal algorithm for sequential data compression
IEEE Transactions on Information Theory
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
Improved grammar-based compressed indexes
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
RCSI: scalable similarity search in thousand(s) of genomes
Proceedings of the VLDB Endowment
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Recent advances in biotechnology and web technology are generating huge collections of similar strings. People now face the problem of storing them compactly while supporting fast pattern searching. One compression scheme called relative Lempel-Ziv compression uses textual substitutions from a reference text as follows: Given a (large) set S of strings, represent each string in S as a concatenation of substrings from a reference string R . This basic scheme gives a good compression ratio when every string in S is similar to R , but does not provide any pattern searching functionality. Here, we describe a new data structure that supports fast pattern searching.