Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
High-order entropy-compressed text indexes
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
Opportunistic data structures with applications
FOCS '00 Proceedings of the 41st Annual Symposium on Foundations of Computer Science
Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
Fast and space efficient string kernels using suffix arrays
ICML '06 Proceedings of the 23rd international conference on Machine learning
ACM Computing Surveys (CSUR)
A taxonomy of suffix array construction algorithms
ACM Computing Surveys (CSUR)
Rank and select revisited and extended
Theoretical Computer Science
The affix array data structure and its applications to RNA secondary structure analysis
Theoretical Computer Science
Space-efficient static trees and graphs
SFCS '89 Proceedings of the 30th Annual Symposium on Foundations of Computer Science
The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and Pattern Matching
The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and 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
High Throughput Short Read Alignment via Bi-directional BWT
BIBM '09 Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine
Pattern discovery in RNA secondary structure using affix trees
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
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
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Searching for genes encoding microRNAs (miRNAs) is an important task in genome analysis. Because the secondary structure of miRNA (but not the sequence) is highly conserved, the genes encoding it can be determined by finding regions in a genomic DNA sequence that match the structure. It is known that algorithms using a bidirectional search on the DNA sequence for this task outperform algorithms based on unidirectional search. The data structures supporting a bidirectional search (affix trees and affix arrays), however, are rather complex and suffer from their large space consumption. Here, we present a new data structure called bidirectional wavelet index that supports bidirectional search with much less space. With this data structure, it is possible to search for candidates of RNA secondary structural patterns in large genomes, for example the complete human genome. Another important application of this data structure is short read alignment. As a second contribution, we show how bidirectional matching statistics can be computed in linear time.