Cited by 9,374Genomics and Phylogenetic StudiesFractal and DNA sequence analysisAlgorithms and Data Compression

Tandem repeats finder: a program to analyze DNA sequences

Open access
Benson, G.·1999·Nucleic Acids Research

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.

Integrity signals

Registry

Crossref · 10.1093/nar/27.2.573

Cites

33 of 33 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Orthology can be established for 94,452 out of the 98,021 VNTR loci (96.4%) discovered by TRF.

    “The orthology can be established for 94,452 out of the 98,021 VNTR loci (96.4%) discovered by TRF56.”

    From A draft human pangenome reference. (2023) · cites this paper as [56]

  • Tandem repeat regions were enriched in known polymorphic simple sequence repeat regions (OR=6.24; p<2.2×10−16).

    “they were prevalent in known polymorphic simple sequence repeat regions previously detected by Tandem Repeats Finder35 in 1,031,708 locations in the human reference genome (odds ratio (OR)=6.24; p<2.2×10−16)36.”

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Benson, G.
Affiliations
Icahn School of Medicine at Mount Sinai (US)
Corresponding author
Benson, G.
Venue
Nucleic Acids Research
Published
1999-01-01
Volume
27
Issue
2
Pages
573-580
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
OpenAlex
W2112814753
Cited by
9,374
References
32
Citations by year
2026: 682 · 2025: 881 · 2024: 960 · 2023: 724 · 2022: 762 · 2021: 794 · 2020: 525 · 2019: 450 · 2018: 368 · 2017: 318 · 2016: 300 · 2015: 256 · 2014: 279 · 2013: 229 · 2012: 259
FWCI
12.06
Type
journal article
Language
en
Open access
Locations
  • Nucleic Acids Research (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
National Science Foundation
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
  • Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
Keywords
tandem repeats, tandem repeat detection, DNA sequence analysis, indel frequency, trinucleotide repeat expansion, frataxin gene, yeast chromosomes, web server
MeSH terms
Frataxin, Algorithms, Friedreich Ataxia, Genes, Fungal, Humans, Membrane Proteins, Mutation, Pattern Recognition, Automated, Probability, Pseudogenes, Software, Models, Statistical, Chromosomes, Fungal, Cluster Analysis, Receptors, Antigen, T-Cell, alpha-beta, Sequence Analysis, DNA, Phosphotransferases (Alcohol Group Acceptor), Tandem Repeat Sequences, Saccharomyces cerevisiae Proteins, Iron-Binding Proteins, Mannose-Binding Lectins

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review