Tandem repeats finder: a program to analyze DNA sequences
Open accessAbstract
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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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.”
From Genome-wide detection of tandem DNA repeats that are expanded in autism (2020) · cites this paper as [35]
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- Authors
- Benson, G.
- Affiliations
- Icahn School of Medicine at Mount Sinai (US)
- Corresponding author
- Benson, G.
- ORCID
- Benson, G.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1999-01-01
- Volume
- 27
- Issue
- 2
- Pages
- 573-580
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC148217
- 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
- green
- europepmc.org
- 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
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