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Nucleic Acids Research, Vol 27, Issue 2 573-580, Copyright © 1999 by Oxford University Press


ARTICLES

Tandem repeats finder: a program to analyze DNA sequences

G Benson
Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, NY 10029-6574, USA. benson@ecology.biomath.mssm.edu

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.
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DiabetesHome page
R. H. Wallis, K. Wang, D. Dabrowski, L. Marandi, T. Ning, E. Hsieh, A. D. Paterson, J. P. Mordes, E. P. Blankenhorn, and P. Poussier
A Novel Susceptibility Locus on Rat Chromosome 8 Affects Spontaneous but Not Experimentally Induced Type 1 Diabetes
Diabetes, June 1, 2007; 56(6): 1731 - 1736.
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GeneticsHome page
L. N. Kwong, A. Shedlovsky, B. S. Biehl, L. Clipson, C. A. Pasch, and W. F. Dove
Identification of Mom7, a Novel Modifier of ApcMin/+ on Mouse Chromosome 18
Genetics, June 1, 2007; 176(2): 1237 - 1244.
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BioinformaticsHome page
S. B. Mudunuri and H. A. Nagarajaram
IMEx: Imperfect Microsatellite Extractor
Bioinformatics, May 15, 2007; 23(10): 1181 - 1187.
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J. Med. Genet.Home page
K. Debacker, B. Winnepenninckx, N. Ben-Porat, D. FitzPatrick, R. Van Luijk, S. Scheers, B. Kerem, and R Frank Kooy
FRA18C: a new aphidicolin-inducible fragile site on chromosome 18q22, possibly associated with in vivo chromosome breakage
J. Med. Genet., May 1, 2007; 44(5): 347 - 352.
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BioinformaticsHome page
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.
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Circ. Res.Home page
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.
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Genome ResHome page
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.
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Eukaryot CellHome page
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.
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Genome ResHome page
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.
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BioinformaticsHome page
A. K. Brodzik
Quaternionic periodicity transform: an algebraic solution to the tandem repeat detection problem
Bioinformatics, March 15, 2007; 23(6): 694 - 700.
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MicrobiologyHome page
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.
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MicrobiologyHome page
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.
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The Computer JournalHome page
A. Bakalis, C.S. Iliopoulos, C. Makris, S. Sioutas, E. Theodoridis, A. Tsakalidis, and K. Tsichlas
Locating Maximal Multirepeats in Multiple Strings Under Various Constraints
The Computer Journal, March 1, 2007; 50(2): 178 - 185.
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Genome ResHome page
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.
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BioinformaticsHome page
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.
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GeneticsHome page
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.
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