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Nucleic Acids Research
Article . 1999 . Peer-reviewed
Data sources: Crossref
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Nucleic Acids Research
Article
License: implied-oa
Data sources: UnpayWall
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Tandem repeats finder: a program to analyze DNA sequences

Authors: G, Benson;

Tandem repeats finder: a program to analyze DNA sequences

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 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.

Related Organizations
Keywords

Models, Statistical, Saccharomyces cerevisiae Proteins, Receptors, Antigen, T-Cell, alpha-beta, Genes, Fungal, Membrane Proteins, Sequence Analysis, DNA, Pattern Recognition, Automated, Phosphotransferases (Alcohol Group Acceptor), Mannose-Binding Lectins, Friedreich Ataxia, Tandem Repeat Sequences, Iron-Binding Proteins, Mutation, Cluster Analysis, Humans, Chromosomes, Fungal, Algorithms, Pseudogenes, Software, Probability

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
8K
Top 0.01%
Top 0.01%
Top 1%
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