Tandem repeats finder: a program to analyze DNA sequences

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ID: 289270
1999
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Abstract
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 β T cell receptor locus sequence and two yeast chromosomes. These sequences range in size from 3 kb up to 700 kb. a world wide web server interface at c3.biomath.mssm.edu/trf.html has been established for automated use of the program.
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openalex_W2112814753 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Gary Benson
Journal Nucleic Acids Research
Year 1999
DOI
10.1093/nar/27.2.573
URL
https://doi.org/10.1093/nar/27.2.573
Keywords Keywords not found

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