Nucleic Acids Research, Vol 27, Issue 2 573-580, Copyright © 1999 by Oxford University Press
G Benson
A tandem repeat in DNA is two or more contiguous, approximate copies of a
pattern of nucleotides. Tandem repeats have been shown to cause human
disease, may play a variety of regulatory and evolutionary roles and are
important laboratory and analytic tools. Extensive knowledge about pattern
size, copy number, mutational history, etc. for tandem repeats has been
limited by the inability to easily detect them in genomic sequence data. In
this paper, we present a new algorithm for finding tandem repeats which
works without the need to specify either the pattern or pattern size. We
model tandem repeats by percent identity and frequency of indels between
adjacent pattern copies and use statistically based recognition criteria.
We demonstrate the algorithm's speed and its ability to detect tandem
repeats that have undergone extensive mutational change by analyzing four
sequences: the human frataxin gene, the human beta T cellreceptor locus
sequence and two yeast chromosomes. These sequences range in size from 3 kb
up to 700 kb. A World Wide Web server interface
atc3.biomath.mssm.edu/trf.html has been established for automated use of
the program.
ARTICLES
Tandem repeats finder: a program to analyze DNA sequences
Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, NY 10029-6574, USA. benson@ecology.biomath.mssm.edu
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A. Caprera, B. Lazzari, A. Stella, I. Merelli, A. R. Caetano, and P. Mariani GoSh: a web-based database for goat and sheep EST sequences Bioinformatics, April 15, 2007; 23(8): 1043 - 1045. [Abstract] [Full Text] [PDF]
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 J.-R. Clemitson, R. J. Dixon, S. Haines, A. J. Bingham, B. R. Patel, L. Hall, M. Lo, J. Sassard, F. J. Charchar, and N. J. Samani Genetic Dissection of a Blood Pressure Quantitative Trait Locus on Rat Chromosome 1 and Gene Expression Analysis Identifies SPON1 As a Novel Candidate Hypertension Gene Circ. Res., April 13, 2007; 100(7): 992 - 999. [Abstract] [Full Text] [PDF]
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Z. Jehan, S. Vallinayagam, S. Tiwari, S. Pradhan, L. Singh, A. Suresh, H. M. Reddy, Y.R. Ahuja, and R. A. Jesudasan Novel noncoding RNA from human Y distal heterochromatic block (Yq12) generates testis-specific chimeric CDC2L2 Genome Res., April 1, 2007; 17(4): 433 - 440. [Abstract] [Full Text] [PDF]
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M. Woolfit, E. Rozpedowska, J. Piskur, and K. H. Wolfe Genome Survey Sequencing of the Wine Spoilage Yeast Dekkera (Brettanomyces) bruxellensis Eukaryot. Cell, April 1, 2007; 6(4): 721 - 733. [Abstract] [Full Text] [PDF]
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M. Babcock, S. Yatsenko, P. Stankiewicz, J. R. Lupski, and B. E. Morrow AT-rich repeats associated with chromosome 22q11.2 rearrangement disorders shape human genome architecture on Yq12 Genome Res., April 1, 2007; 17(4): 451 - 460. [Abstract] [Full Text] [PDF]
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A. K. Brodzik Quaternionic periodicity transform: an algebraic solution to the tandem repeat detection problem Bioinformatics, March 15, 2007; 23(6): 694 - 700. [Abstract] [Full Text] [PDF]
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 S. Goh, P. F. Ong, K. P. Song, T. V. Riley, and B. J. Chang The complete genome sequence of Clostridium difficile phage {phi}C2 and comparisons to {phi}CD119 and inducible prophages of CD630 Microbiology, March 1, 2007; 153(3): 676 - 685. [Abstract] [Full Text] [PDF]
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A.-M. Patch and S. J. Aves Fingerprinting fission yeast: polymorphic markers for molecular genetic analysis of Schizosaccharomyces pombe strains Microbiology, March 1, 2007; 153(3): 887 - 897. [Abstract] [Full Text] [PDF]
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K.-H. Ling, M.-A. Rajandream, P. Rivailler, A. Ivens, S.-J. Yap, A. M.B.N. Madeira, K. Mungall, K. Billington, W.-Y. Yee, A. T. Bankier, et al. Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization Genome Res., March 1, 2007; 17(3): 311 - 319. [Abstract] [Full Text] [PDF]
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L. Du, H. Zhou, and H. Yan OMWSA: detection of DNA repeats using moving window spectral analysis Bioinformatics, March 1, 2007; 23(5): 631 - 633. [Abstract] [Full Text] [PDF]
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X. H. Hu, M. H. Wang, T. Tan, J. R. Li, H. Yang, L. Leach, R. M. Zhang, and Z. W. Luo Genetic Dissection of Ethanol Tolerance in the Budding Yeast Saccharomyces cerevisiae Genetics, March 1, 2007; 175(3): 1479 - 1487. [Abstract] [Full Text] [PDF]
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