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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|
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|
|
|
|
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|
|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
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|
|
|
|
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|
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|
|
|
|
|
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|
|
|
|
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|
|
|
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