An O(n log n) algorithm for finding all repetitions in a string
Journal of Algorithms
Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version)
CPM '98 Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching
Opportunistic data structures with applications
FOCS '00 Proceedings of the 41st Annual Symposium on Foundations of Computer Science
Application of the burrows-wheeler transform for searching for approximate tandem repeats
PRIB'12 Proceedings of the 7th IAPR international conference on Pattern Recognition in Bioinformatics
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Genomic sequences contain a variety of repeated structures of various lengths and types, interspersed or in tandem. Repetitive structures play an important role in molecular biology; they are related to the genetic backgrounds of inherited diseases, and they can also serve as markers for DNA mapping and DNA fingerprinting. Since biological databases keep growing in size and number there is a need for creating new tools for finding repeats in genomic sequences. This paper presents a new method for searching for tandem repeats in DNA sequences. It is based on the Burrows-Wheeler Transform (BWT), a very fast and effective data compression algorithm.