The DOI matches its Crossref record; 33 of the 33 references it cites were found in a registry or an index.
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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In the citing paper
“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]
In the citing paper
“Despite this diversity, the majority of these databases rely on the results of well-established automated bioinformatic approaches such as the Tandem Repeats Finder (TRF) program (130) or RepeatMasker (118) to characterize repeat content.”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [130]
In the citing paper
“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]
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
An introduction to probability theory and its applications
(1958) · Journal of the Franklin Institute · doi:10.1016/0016-0032(58)90688-4 · Cited by 29,621
Improved tools for biological sequence comparison.
Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227
MACDONALD, M. (1993) · Cell · doi:10.1016/0092-8674(93)90585-e · Cited by 8,366
The American Journal of Human Genetics
S., J. (1950) · Population · doi:10.2307/1523704 · Cited by 5,124
Verkerk, A. J. M. H., Pieretti, M., Sutcliffe, J. S., Fu, Y.-H., Kuhl, D. P. A., Pizzuti, A., Reiner, O., Richards, S., Victoria, M. F., Zhang, F., et al. (1991) · Cell · doi:10.1016/0092-8674(91)90397-h · Cited by 3,481
Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction.
Weber, J. L., & May, P. E. (1989) · Europe PMC (PubMed Central) · Cited by 3,399
Androgen receptor gene mutations in X-linked spinal and bulbar muscular atrophy
Spada, A. L., Wilson, E. M., Lubahn, D. B., Harding, A., & Fischbeck, K. (1991) · Nature · doi:10.1038/352077a0 · Cited by 2,801
Friedreich's Ataxia: Autosomal Recessive Disease Caused by an Intronic GAA Triplet Repeat Expansion
Campuzano, V., Montermini, L., Moltò, M. D., Pianese, L., Cossée, M., Cavalcanti, F., Monros, E., Rodius, F., Duclos, F., Monticelli, A., et al. (1996) · Science · doi:10.1126/science.271.5254.1423 · Cited by 2,786
An Unstable Triplet Repeat in a Gene Related to Myotonic Muscular Dystrophy
Fu, Y., Pizzuti, A., Fenwick, R. G., King, J., Rajnarayan, S., Dunne, P. W., Dubel, J., Nasser, G. A., Ashizawa, T., de Jong, P., et al. (1992) · Science · doi:10.1126/science.1546326 · Cited by 1,453
Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups
Edwards, A., Hammond, H. A., Li, J., Caskey, C. T., & Chakraborty, R. (1992) · Genomics · doi:10.1016/0888-7543(92)90371-x · Cited by 1,426
Global Patterns of Linkage Disequilibrium at the CD4 Locus and Modern Human Origins
Tishkoff, S. A., Dietzsch, E., Speed, W., Pakstis, A. J., Kidd, J. R., Cheung, K., Bonné-Tamir, B., Santachiara-Benerecetti, A. S., Moral, P., Krings, M., et al. (1996) · Science · doi:10.1126/science.271.5254.1380 · Cited by 587
The Complete 685-Kilobase DNA Sequence of the Human β T Cell Receptor Locus
Rowen, L., Koop, B. F., & Hood, L. (1996) · Science · doi:10.1126/science.272.5269.1755 · Cited by 444
Molecular Basis of Genetic Instability of Triplet Repeats
Wells, R. D. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.6.2875 · Cited by 303
Enhanced Gene Expression by the Poly(dT-dG) · Poly(dC-dA) Sequence
Hamada, H., Seidman, M. A., Howard, B. H., & Gorman, C. (1984) · Molecular and Cellular Biology · doi:10.1128/mcb.4.12.2622 · Cited by 293
Lu, Q. R., Wallrath, L. L., Granok, H., & Elgin, S. C. R. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.5.2802 · Cited by 247
Approximate matching of regular expressions
Myers, E. W., & MILLER, W. (1989) · Bulletin of Mathematical Biology · doi:10.1016/s0092-8240(89)80046-1 · Cited by 186
Minisatellite diversity supports a recent African origin for modern humans
Armour, J. A. L., Anttinen, T., May, C. A., Vega, E., Sajantila, A., Kidd, J. R., Kídd, K. K., Bertranpetit, J., Pääbo, S., & Jeffreys, A. J. (1996) · Nature Genetics · doi:10.1038/ng0696-154 · Cited by 164
Schmidt, J. P. (1998) · SIAM Journal on Computing · doi:10.1137/s0097539795288489 · Cited by 157
Pardue, M. L., Lowenhaupt, K., Rich, A., & Nordheim, A. (1987) · The EMBO Journal · doi:10.1002/j.1460-2075.1987.tb02431.x · Cited by 154
Richards, R. I., Holman, K., Yu, S.-L., & Sutherland, G. R. (1993) · Human Molecular Genetics · doi:10.1093/hmg/2.9.1429 · Cited by 129
Approximate matching of regular expressions
Myers, E. W., & Miller, W. (1989) · Bulletin of Mathematical Biology · doi:10.1007/bf02458834 · Cited by 105
On discrete distributions of orderk
Aki, S., Kuboki, H., & Hirano, K. (1984) · Annals of the Institute of Statistical Mathematics · doi:10.1007/bf02481981 · Cited by 99
A method for fast database search for allk-nucleotide repeats
Benson, G., & Waterman, M. S. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4828 · Cited by 77
Self-citationDNA Secondary Structures and the Evolution of Hypervariable Tandem Arrays
Woodford, K. J., Usdin, K., & Weitzmann, M. N. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.14.9517 · Cited by 74
Identification of novel single-stranded d(TC)nbinding proteins in several mammalian species
Yee, H. A., Wong, A. K. C., van de Sande, J. H., & Rattner, J. B. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.4.949 · Cited by 59
An Algorithm for Locating Nonoverlapping Regions of Maximum Alignment Score
Kannan, S. K., & Myers, E. W. (1996) · SIAM Journal on Computing · doi:10.1137/s0097539794262677 · Cited by 55
Efficient algorithms for molecular sequence analysis.
Karlin, S., Morris, M. S., Ghandour, G., & Leung, M. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.3.841 · Cited by 49
A space efficient algorithm for finding the best nonoverlapping alignment score
Benson, G. (1995) · Theoretical Computer Science · doi:10.1016/0304-3975(95)92848-r · Cited by 49
Self-citationSequence Alignment with Tandem Duplication
Benson, G. (1997) · Journal of Computational Biology · doi:10.1089/cmb.1997.4.351 · Cited by 49
Self-citationHellman, L., Steén, M.-L., Sundvall, M., & Pettersson, U. (1988) · Gene · doi:10.1016/0378-1119(88)90602-6 · Cited by 25
Du, J. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.15.3066 · Cited by 24
Benson, G., & Su, X. (1998) · J. Comput. Biol. · doi:10.1089/cmb.1998.5.87 · Cited by 10
Self-citation
Research works printed but not linked: 4
- 1988, 68, 93
- 1993, CABIOS, 9, 407
- 1997, CABIOS, 13, 131
- 1998, Journal of computational biology : a journal of computational molecular cell biology, 5, 87, 10.1089/cmb.1998.5.87 · DOI
Cited by
Sorted by citations
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
Genome sequence of the human malaria parasite Plasmodium falciparum
Gardner, M. J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R. W., Carlton, J. M., Pain, A., Nelson, K. E., Bowman, S., et al. (2002) · Nature · doi:10.1038/nature01097 · Cited by 4,407
Molecular and genetic properties of tumors associated with local immune cytolytic activity
Rooney, M. S., Shukla, S. A., Wu, C. J., Getz, G., & Hacohen, N. (2015) · Cell · doi:10.1016/j.cell.2014.12.033 · Cited by 3,825
Repbase Update, a database of eukaryotic repetitive elements
Jurka, J., Kapitonov, V. V., Pavlíček, A., Klonowski, P., Kohany, O., & Walichiewicz, J. (2005) · Cytogenetic and Genome Research · doi:10.1159/000084979 · Cited by 3,413
MISA-web: a web server for microsatellite prediction
Beier, S., Thiel, T., Münch, T., Scholz, U., & Mascher, M. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx198 · Cited by 2,644
Metadata
- 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 › Mathematics › Theoretical Computer Science › 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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