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

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 access

Benson, G.·1999·Nucleic Acids Research

Open this paper in CoChat — free account

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?

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
A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes
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
Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome
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

Show all 32 references

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

Sorted by citations

Items 701–800 of 1,021

A Genomic Portrait of Human Microsatellite Variation
Payseur, B. A., Jing, P., & Haasl, R. J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq198 · Cited by 106
Know your farmer: Ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars
Vanderpool, D., Bracewell, R., & McCutcheon, J. P. (2017) · Molecular Ecology · doi:10.1111/mec.14394 · Cited by 105
A reassessment of DNA-immunoprecipitation-based genomic profiling
Lentini, A., Lagerwall, C., Vikingsson, S., Mjoseng, H. K., Douvlataniotis, K., Vogt, H., Gréen, H., Meehan, R. R., Benson, M., & Nestor, C. E. (2018) · Nature Methods · doi:10.1038/s41592-018-0038-7 · Cited by 105
The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence
Huang, X., Wang, W., Gong, T., Wickell, D., Kuo, L., Zhang, X., Wen, J., Kim, H., Lu, F., Zhao, H., et al. (2022) · Nature Plants · doi:10.1038/s41477-022-01146-6 · Cited by 106
CAG-encoded polyglutamine length polymorphism in the human genome
Butland, S., Devon, R. S., Huang, Y., Mead, C.-L., Meynert, A., Neal, S. J., Lee, S.-S., Wilkinson, A., Yang, G. S., Yuen, M. M., et al. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-126 · Cited by 90
Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesisPreprint
Bogdanović, O., Long, S. W., van Heeringen, S. J., Brinkman, A. B., Skarmeta, J. L. G., Stunnenberg, H. G., Jones, P. L., & Veenstra, G. J. C. (2011) · Genome Research · doi:10.1101/gr.114843.110 · Cited by 105
Characterization of the Complete Mitochondrial Genomes of Cnaphalocrocis medinalis and Chilo suppressalis (Lepidoptera: Pyralidae)
Chai, H.-N., Du, Y., & Zhai, B. (2012) · International Journal of Biological Sciences · doi:10.7150/ijbs.3540 · Cited by 102
Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance
Lim, K. G., Kwoh, C. K., Hsu, L. Y., & Wirawan, A. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs023 · Cited by 102
Complete Chloroplast Genome Sequence of Poisonous and Medicinal Plant Datura stramonium: Organizations and Implications for Genetic Engineering
Yang, Y., Dang, Y.-Y., Li, Q., Lu, J.-J., Li, X.-W., & Wang, Y.-T. (2014) · PLoS ONE · doi:10.1371/journal.pone.0110656 · Cited by 70
Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta
Lee, J., Yang, E. C., Graf, L., Yang, J. H., Qiu, H., Zelzion, U., Chan, C. X., Stephens, T. G., Weber, A. P. M., Boo, G. H., et al. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy081 · Cited by 103
Multiple convergent supergene evolution events in mating-type chromosomes
Branco, S., Carpentier, F., de la Vega, R. C. R., Badouin, H., Snirc, A., Prieur, S. L., Coelho, M. A., de Vienne, D. M., Hartmann, F. E., Begerow, D., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04380-9 · Cited by 99
Targeted molecular mapping of a major wheat QTL forFusariumhead blight resistance using wheat ESTs and synteny with rice
Liu, S., & Anderson, J. A. (2003) · Genome · doi:10.1139/g03-066 · Cited by 102
Survey of repetitive sequences in Silene latifolia with respect to their distribution on sex chromosomes
Čermák, T., Kubát, Z., Hobza, R., Koblížková, A., Widmer, A., Macas, J., Vyskot, B., & Kejnovský, E. (2008) · Chromosome Research · doi:10.1007/s10577-008-1254-2 · Cited by 102
Differentially Expressed and Secreted Major Immunoreactive Protein Orthologs of Ehrlichia canis and E. chaffeensis Elicit Early Antibody Responses to Epitopes on Glycosylated Tandem Repeats
Doyle, C. K., Nethery, K. A., Popov, V. L., & McBride, J. W. (2005) · Infection and Immunity · doi:10.1128/iai.74.1.711-720.2006 · Cited by 102
Discovery of Highly Divergent Repeat Landscapes in Snake Genomes Using High-Throughput Sequencing
Castoe, T. A., Hall, K. T., Mboulas, M. L. G., Gu, W., de Koning, A. P. J., Fox, S. E., Poole, A. W., Vemulapalli, V., Daza, J. M., Mockler, T. C., et al. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr043 · Cited by 102
A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres
Ellwood, S. R., Liu, Z., Syme, R. A., Lai, Z., Hane, J. K., KEIPER, F. J., Moffat, C. S., Oliver, R. P., & Friesen, T. L. (2010) · Genome biology · doi:10.1186/gb-2010-11-11-r109 · Cited by 102
Sequence Divergence Within Transposable Element Families in the Drosophila melanogaster Genome
Lerat, E., Rizzon, C., & Biémont, C. (2003) · Genome Research · doi:10.1101/gr.827603 · Cited by 81
A Genome-wide Comparison of the Functional Properties of Rare and Common Genetic Variants in Humans
Zhu, Q., Ge, D., Maia, J. M., Zhu, M., Petrovski, S., Dickson, S. P., Heinzen, E. L., Shianna, K. V., & Goldstein, D. B. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.03.008 · Cited by 96
The genome of the vervet (Chlorocebus aethiops sabaeus)
Warren, W. C., Jasinska, A. J., García-Pérez, R., Svardal, H., Tomlinson, C., Rocchi, M., Archidiacono, N., Capozzi, O., Minx, P., Montague, M. J., et al. (2015) · Genome Research · doi:10.1101/gr.192922.115 · Cited by 123
Genome Structures and Halophyte-Specific Gene Expression of the Extremophile Thellungiella parvula in Comparison with Thellungiella salsuginea ( Thellungiella halophila ) and Arabidopsis
Oh, D., Dassanayake, M., Haas, J. S., Kropornika, A., Wright, C. L., D’Urzo, M. P., Hong, H., Ali, S., Hernandez, A. G., Lambert, G. M., et al. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.110.163923 · Cited by 101
The complete mitochondrial genomes of three parasitic nematodes of birds: a unique gene order and insights into nematode phylogeny
Liu, G., Shao, R., Li, J.-Y., Zhou, D., Li, H., & Zhu, X. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-414 · Cited by 101
The genome of the miiuy croaker reveals well-developed innate immune and sensory systems
Xu, T., Xu, G., Che, R., Wang, R., Wang, Y., Li, J., Wang, S., Shu, C., Sun, Y., Liu, T., et al. (2016) · Scientific Reports · doi:10.1038/srep21902 · Cited by 101
A draft genome of the brown alga,Cladosiphon okamuranus, S-strain: a platform for future studies of ‘mozuku’ biology
Nishitsuji, K., Arimoto, A., Iwai, K., Sudo, Y., Hisata, K., Fujie, M., Arakaki, N., Kushiro, T., Konishi, T., Shinzato, C., et al. (2016) · DNA Research · doi:10.1093/dnares/dsw039 · Cited by 100
Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach
Mayer, C., Leese, F., & Tollrian, R. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-277 · Cited by 100
Coding potential and transcript analysis of fowl adenovirus 4: insight into upstream ORFs as common sequence features in adenoviral transcripts
Griffin, B. D., & Nagy, É. (2011) · Journal of General Virology · doi:10.1099/vir.0.030064-0 · Cited by 101
A Hypervariable Invertebrate Allodeterminant
Nicotra, M. L., Powell, A. E., Rosengarten, R. D., Moreno, M. A., Grimwood, J., Lakkis, F. G., Dellaporta, S. L., & Buss, L. W. (2009) · Current Biology · doi:10.1016/j.cub.2009.02.040 · Cited by 100
Multi-locus variable-number tandem repeat analysis for outbreak studies of Salmonella enterica serotype Enteritidis
Malorny, B., Junker, E., & Helmuth, R. (2008) · BMC Microbiology · doi:10.1186/1471-2180-8-84 · Cited by 100
High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps
Georges, A., Li, Q., Lian, J., O’Meally, D., Deakin, J. E., Wang, Z., Zhang, P., Fujita, M. K., Patel, H. R., Holleley, C. E., et al. (2015) · GigaScience · doi:10.1186/s13742-015-0085-2 · Cited by 101
Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes
Zhou, P., Silverstein, K. A. T., Ramaraj, T., Guhlin, J. G., Denny, R. L., Liu, J., Farmer, A. D., Steele, K. P., Stupar, R. M., Miller, J. R., et al. (2017) · BMC Genomics · doi:10.1186/s12864-017-3654-1 · Cited by 102
The Polycomb protein Ezl1 mediates H3K9 and H3K27 methylation to repress transposable elements in Paramecium
Frapporti, A., Miró-Pina, C., Arnaiz, O., Holoch, D., Kawaguchi, T., Humbert, A., Eleftheriou, E., Lombard, B., Loew, D., Sperling, L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10648-5 · Cited by 104
Long-read sequencing for rare human genetic diseases
Mitsuhashi, S., & Matsumoto, N. (2019) · Journal of Human Genetics · doi:10.1038/s10038-019-0671-8 · Cited by 105
Genomic consequences of population decline in critically endangered pangolins and their demographic histories
Hu, J., Hao, Z.-Q., Frantz, L., Wu, S., Wu, C., Jiang, Y.-F., Wu, H., Kuang, W., Li, H., Zhang, Y., et al. (2020) · National Science Review · doi:10.1093/nsr/nwaa031 · Cited by 107
Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing
Hřibová, E., Neumann, P., Matsumoto, T., Roux, N., Macas, J., & Doležel, J. (2010) · BMC Plant Biology · doi:10.1186/1471-2229-10-204 · Cited by 100
Development and Characterization of Microsatellite Markers for the Grain Amaranths
Mallory, M. A., Hall, R. V., McNabb, A. R., Pratt, D. B., Jellen, E. N., & Maughan, P. J. (2008) · Crop Science · doi:10.2135/cropsci2007.08.0457 · Cited by 100
Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13)Preprint
Gajęcka, M., Gentles, A. J., Tsai, A. G., Chitayat, D. A., Mackay, K. L., Glotzbach, C. D., Lieber, M. R., & Shaffer, L. G. (2008) · Genome Research · doi:10.1101/gr.077453.108 · Cited by 100
A call for benchmarking transposable element annotation methods
Hoen, D. R., Hickey, G., Bourque, G., Casacuberta, J., Cordaux, R., Feschotte, C., Fiston-Lavier, A.-S., Hua-Van, A., Hubley, R., Kapusta, A., et al. (2015) · Mobile DNA · doi:10.1186/s13100-015-0044-6 · Cited by 105
Genome sequencing and comparative genomics of honey bee microsporidia, Nosema apis reveal novel insights into host-parasite interactions
Chen, Y. P., Pettis, J. S., Zhao, Y., Liu, X., Tallon, L. J., Sadzewicz, L., Li, R., Zheng, H., Huang, S., Zhang, X., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-451 · Cited by 99
Complete chloroplast genome sequences of four Allium species: comparative and phylogenetic analyses
Huo, Y., Gao, L., Liu, B., Yang, Y.-Y., Kong, S., Sun, Y., Yang, Y., & Wu, X. (2019) · Scientific Reports · doi:10.1038/s41598-019-48708-x · Cited by 99
The chromosome-level reference genome assembly for Dendrobium officinale and its utility of functional genomics research and molecular breeding study
Niu, Z., Zhu, F., Fan, Y., Li, C., Zhang, B., Zhu, S., Hou, Z., Wang, M., Yang, J., Xue, Q., et al. (2021) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2021.01.019 · Cited by 101
Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits
Long, R., Zhang, F., Zhang, Z., Li, M., Chen, L., Wang, X., Liu, W., Zhang, T., Yu, L., He, F., et al. (2022) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2022.01.002 · Cited by 99
“09) was used to detect tandem repeats [56].”
Method
The chromosome-scale genome of Phoebe bournei reveals contrasting fates of terpene synthase (TPS)-a and TPS-b subfamilies
Han, X., Zhang, J., Han, S., Chong, S. L., Meng, G., Song, M., Wang, Y., Zhou, S., Liu, C., Lou, L., et al. (2022) · Plant Communications · doi:10.1016/j.xplc.2022.100410 · Cited by 99
“For the first method, two databases, Repbase (Bao et al., 2015) and PGSB-REdat (Spannagl et al., 2016), were used for annotation with RepeatMasker v.4.0.8 (Bedell et al., 2000), RepeatProteinMask (Bedell et al., 2000), and Tandem repeats finder (Benson, 1999).”
MethodInfluential
Microsatellites within genes and ESTs of common carp and their applicability in silver crucian carp
Yue, G. H., Ho, M. Y., Orbán, L., & Komen, J. (2004) · Aquaculture · doi:10.1016/j.aquaculture.2003.12.021 · Cited by 99
Sequence and expression analysis of two T helper master transcription factors, T-bet and GATA3, in rainbow trout Oncorhynchus mykiss and analysis of their expression during bacterial and parasitic infection☆
Wang, T., Holland, J. W., Martín, S., & Secombes, C. J. (2010) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2010.06.016 · Cited by 99
The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment
Shin, S. C., Ahn, D., Kim, S. J., Pyo, C., Lee, H., Kim, M.-K., Lee, J., Lee, J., Detrich, H. W., Postlethwait, J. H., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0468-1 · Cited by 99
The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet
Liu, H., Chen, C., Gao, Z., Min, J., Gu, Y., Jiang, X., Jiang, X., Cai, H., Ebersberger, I., Xu, M., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix039 · Cited by 98
Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition
Pavlı́ček, A., Noskov, V. N., Kouprina, N., Barrett, J. C., Jurka, J., & Larionov, V. (2004) · Human Molecular Genetics · doi:10.1093/hmg/ddh301 · Cited by 100
Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe setPreprint
Damas, J., O’Connor, R. E., Farré, M., Lenis, V. P. E., Martell, H. J., Mandawala, A. A., Fowler, K. E., Joseph, S., Swain, M., Griffin, D. K., et al. (2016) · Genome Research · doi:10.1101/gr.213660.116 · Cited by 103
Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation
Kidd, J. M., Gravel, S., Byrnes, J., Moreno-Estrada, A., Musharoff, S., Bryc, K., Degenhardt, J. D., Brisbin, A., Sheth, V., Chen, R., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.08.025 · Cited by 95
Genome-wide profiling of Populus small RNAs
Klevebring, D., Street, N. R., Fahlgren, N., Kasschau, K. D., Carrington, J. C., Lundeberg, J., & Jansson, S. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-620 · Cited by 98
Biophysical and Population Genetic Models Predict the Presence of “Phantom” Stepping Stones Connecting Mid-Atlantic Ridge Vent Ecosystems
Breusing, C., Biastoch, A., Drews, A., Metaxas, A., Jollivet, D., Vrijenhoek, R. C., Bayer, T., Melzner, F., Sayavedra, L., Petersen, J. M., et al. (2016) · Current Biology · doi:10.1016/j.cub.2016.06.062 · Cited by 97
A high‐quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance
Chen, X.-Q., Tong, C., Zhang, X.-T., Song, A.-X., Hu, M., Dong, W., Chen, F., Wang, Y.-P., Tu, J., Liu, S.-Y., et al. (2020) · Plant Biotechnology Journal · doi:10.1111/pbi.13493 · Cited by 83
Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition
Zhuang, Y., Wang, X., Li, X., Hu, J., Fan, L., Landis, J. B., Cannon, S. B., Grimwood, J., Schmutz, J., Jackson, S. A., et al. (2022) · Nature Plants · doi:10.1038/s41477-022-01102-4 · Cited by 94
Complete Mitochondrial Genome of the Medicinal Mushroom Ganoderma lucidum
Li, J., Zhang, J., Chen, H., Chen, X., Lan, J., & Liu, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0072038 · Cited by 98
Annotating eukaryote genomes
Lewis, S., Ashburner, M., & Reese, M. G. (2000) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00095-6 · Cited by 98
Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes
Cer, R. Z., Bruce, K. H., Mudunuri, U. S., Yi, M., Volfovsky, N., Luke, B. T., Bacolla, A., Collins, J., & Stephens, R. M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1170 · Cited by 98
Differentiation of Strains of Xylella fastidiosa by a Variable Number of Tandem Repeat Analysis
Coletta-Filho, H. D., Takita, M. A., de Souza, A. A., Aguilar-Vildoso, C. I., & Machado, M. A. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.9.4091-4095.2001 · Cited by 98
Whole genome sequencing of Brucella melitensis isolated from 57 patients in Germany reveals high diversity in strains from Middle East
Georgi, E., Walter, M. C., Pfalzgraf, M.-T., Northoff, B. H., Holdt, L. M., Scholz, H. C., Zoeller, L., Zange, S., & Antwerpen, M. H. (2017) · PLoS ONE · doi:10.1371/journal.pone.0175425 · Cited by 98
Integrating multiple evidence sources to predict transcription factor binding in the human genomePreprint
Ernst, J., Plasterer, H. L., Simon, I., & Bar-Joseph, Z. (2010) · Genome Research · doi:10.1101/gr.096305.109 · Cited by 97
The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology
Derks, M. F. L., Smit, S., Salis, L., Schijlen, E. G. W. M., Bossers, A., Mateman, A. C., Pijl, A. S., de Ridder, D., Groenen, M. A. M., Visser, M. E., et al. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv145 · Cited by 98
High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree
Smeds, L., Mugal, C. F., Qvarnström, A., & Ellegren, H. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006044 · Cited by 103
Genome sequence of the corn leaf aphid ( Rhopalosiphum maidis Fitch)
Chen, W., Shakir, S., Bigham, M., Richter, A., Fei, Z., & Jander, G. (2019) · GigaScience · doi:10.1093/gigascience/giz033 · Cited by 97
The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome
Kan, S., Shen, T., Gong, P., Ran, J., & Wang, X. (2020) · BMC Evolutionary Biology · doi:10.1186/s12862-020-1582-1 · Cited by 97
Finding Approximate Tandem Repeats in Genomic Sequences
Wexler, Y., Zohar Yakhini, B., Kashi, Y., & Geiger, D. (2005) · Journal of Computational Biology · doi:10.1089/cmb.2005.12.928 · Cited by 97
Applications of recursive segmentation to the analysis of DNA sequences
Li, W., Bernaola‐Galván, P., Haghighi, F., & Große, I. (2002) · Computers & Chemistry · doi:10.1016/s0097-8485(02)00010-4 · Cited by 98
Quantitative real-time PCR assays for detection and quantification of all seven Eimeria species that infect the chicken
Vrba, V., Blake, D. P., & Poplštein, M. (2010) · Veterinary Parasitology · doi:10.1016/j.vetpar.2010.09.006 · Cited by 97
Activation-Induced Cytidine Deaminase Induces Reproducible DNA Breaks at Many Non-Ig Loci in Activated B Cells
Staszewski, O., Baker, R. E., Ucher, A. J., Martier, R., Stavnezer, J., & Guikema, J. E. J. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.01.007 · Cited by 95
Multilocus Sequence Typing ofLactobacillus caseiReveals a Clonal Population Structure with Low Levels of Homologous Recombination
Diancourt, L., Passet, V., Chervaux, C., Garault, P., Smokvina, T., & Brisse, S. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01095-07 · Cited by 98
Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)
Zhang, G., Tian, Y., Zhang, J., Shu, L., Yang, S., Wang, W., Sheng, J., Dong, Y., & Chen, W. (2015) · GigaScience · doi:10.1186/s13742-015-0104-3 · Cited by 95
The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species
Park, I., Kim, W., Yeo, S.-M., Choi, G., Kang, Y., Piao, R., & Moon, B. C. (2017) · Molecules · doi:10.3390/molecules22060982 · Cited by 97
De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture
Mahajan, S., Wei, K. H.-C., Nalley, M. J., Gibilisco, L., & Bachtrog, D. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2006348 · Cited by 96
Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates
Willems, T., Gymrek, M., Poznik, G. D., Tyler‐Smith, C., The 1000 Genomes Project Chromosome Y Group, & Erlich, Y. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.04.001 · Cited by 104
Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis
Cai, Y.-F., Cai, X.-Y., Wang, Q.-L., Wang, P., Zhang, Y., Cai, C.-W., Xu, Y.-C., Wang, K.-B., Zhou, Z.-L., Wang, C., et al. (2019) · Plant Biotechnology Journal · doi:10.1111/pbi.13249 · Cited by 75
The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia
Song, H., Guo, X., Sun, L., Wang, Q., Han, F., Wang, H., Wray, G. A., Davidson, P. L., Wang, Q., Hu, Z., et al. (2021) · BMC Biology · doi:10.1186/s12915-020-00943-9 · Cited by 94
Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe
Su, W., Jing, Y., Lin, S., Yue, Z., Yang, X., Wu, J., Wu, J., Zhang, Z., Xia, R., Zhu, J., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2101767118 · Cited by 98
“Tandem repeats were searched using Tandem Repeats Finder (59).”
Method
Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
Xue, L., Gao, Y., Wu, M., Tian, T., Fan, H., Huang, Y., Huang, Z. J., Li, D., & Xu, L. (2021) · Genome biology · doi:10.1186/s13059-021-02430-y · Cited by 96
“hap-X and hap-Y contigs, respectively, with the 3D-DNA (180114) pipeline [66, 67].”
Method
Incipient diploidization of the medicinal plant Perilla within 10,000 years
Zhang, Y.-J., Shen, Q., Leng, L., Zhang, D., Chen, S., Shi, Y., Ning, Z., & Chen, S.-L. (2021) · Nature Communications · doi:10.1038/s41467-021-25681-6 · Cited by 85
Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy
Li, M.-H., Liu, K., Li, Z., Lu, H.-C., Ye, Q., Zhang, D., Wang, J., Li, Y., Zhong, Z., Liu, X., et al. (2022) · Nature Plants · doi:10.1038/s41477-022-01127-9 · Cited by 102
Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis
Yue, J., Chen, Q., Wang, Y., Zhang, L., Ye, C., Wang, X., Cao, S., Lin, Y., Huang, W., He, X., et al. (2022) · Horticulture Research · doi:10.1093/hr/uhac264 · Cited by 94
“Using the Tandem Repeats Finder (TRF) tool [26], we first identified whole-genome tandem repeats in our genome assembly.”
MethodInfluential
The internal transcribed spacer of nuclear ribosomal DNA in the gymnosperm Gnetum
Won, H., & Renner, S. S. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2005.03.011 · Cited by 96
High quality reference genome of drumstick tree (Moringa oleifera Lam.), a potential perennial crop
Tian, Y., Zeng, Y., Zhang, J., Yang, C., Yan, L., Wang, X., Shi, C., Xie, J., Dai, T., Peng, L., et al. (2015) · Science China Life Sciences · doi:10.1007/s11427-015-4872-x · Cited by 95
Transcriptome analysis and microsatellite discovery in the blunt snout bream (Megalobrama amblycephala) after challenge with Aeromonas hydrophila
Tran, N. T., Gao, Z., Zhao, H., Yi, S., Chen, B.-X., Zhao, Y., Lin, L., Liu, X., & Wang, W. (2015) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2015.01.034 · Cited by 95
The complete nucleotide sequence of the mitochondrial genome of the cabbage butterfly, Artogeia melete (Lepidoptera: Pieridae)
Hong, G.-Y., Jiang, S., Yu, M., Yang, Y., Li, F., Xue, F., & Wei, Z. (2009) · Acta Biochimica et Biophysica Sinica · doi:10.1093/abbs/gmp030 · Cited by 95
Dynamic turnover of centromeres drives karyotype evolution in Drosophila
Bracewell, R., Chatla, K., Nalley, M. J., & Bachtrog, D. (2019) · eLife · doi:10.7554/elife.49002 · Cited by 95
Biodegradation of phthalate esters by Paracoccus kondratievae BJQ0001 isolated from Jiuqu (Baijiu fermentation starter) and identification of the ester bond hydrolysis enzyme
Xu, Y., Minhazul, K. A. H. M., Wang, X., Liu, X., Li, X., Meng, Q., Li, H., Zhang, C., Sun, X., & Sun, B. (2020) · Environmental Pollution · doi:10.1016/j.envpol.2020.114506 · Cited by 95
Variable number tandem repeats mediate the expression of proximal genes
Bakhtiari, M., Park, J., Ding, Y.-C., Shleizer-Burko, S., Neuhausen, S. L., Halldórsson, B. V., Stefánsson, K., Gymrek, M., & Bafna, V. (2021) · Nature Communications · doi:10.1038/s41467-021-22206-z · Cited by 93
The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts
Wan, T., Liu, Z., Leitch, I. J., Xin, H., Maggs‐Kölling, G., Gong, Y., Li, Z., Marais, E., Liao, Y., Dai, C., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24528-4 · Cited by 95
Genomic insights into the evolution of Echinochloa species as weed and orphan crop
Wu, D., Shen, E., Jiang, B., Feng, Y., Tang, W., Lao, S., Jia, L., Lin, H., Xie, L., Weng, X., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28359-9 · Cited by 100
Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference
Kim, T. S., Booth, J. G., Gauch, H. G., Sun, Q., Park, J., Lee, Y. H., & Lee, K. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-31 · Cited by 95
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression
Boeva, V., Régnier, M., Papatsenko, D., & Makeev, V. J. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btk032 · Cited by 95
Salmon Gill Poxvirus, the Deepest Representative of the Chordopoxvirinae
Gjessing, M. C., Yutin, N., Tengs, T., Senkevich, T. G., Koonin, E. V., Rønning, H. P., Alarcón, M., Ylving, S., Lie, K. I., Saure, B., et al. (2015) · Journal of Virology · doi:10.1128/jvi.01174-15 · Cited by 95
Data Mining and Knowledge Discovery in Real Life Applications
Ponce, J., & Karahoca, A. (2009) · doi:10.5772/97 · Cited by 96
Multiple Polymorphic Loci for Molecular Typing of Strains of Mycobacterium leprae
Groathouse, N. A., Rivoire, B., Kim, H., Lee, H., Cho, S.-N., Brennan, P. J., & Vissa, V. (2004) · Journal of Clinical Microbiology · doi:10.1128/jcm.42.4.1666-1672.2004 · Cited by 95
Sensory physiological basis for attraction in mosquitoes.
Davis, E. E., & Bowen, M. F. (1994) · PubMed · Cited by 95
Genome-wide characterization of centromeric satellites from multiple mammalian genomesPreprint
Alkan, C., Cardone, M. F., Catacchio, C. R., Antonacci, F., O’Brien, S. J., Ryder, O. A., Purgato, S., Zoli, M., Valle, G. D., Eichler, E. E., et al. (2010) · Genome Research · doi:10.1101/gr.111278.110 · Cited by 95
DrosophilaMuller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution
Leung, W., Shaffer, C. D., Reed, L. K., Smith, S. T., Barshop, W. D., Dirkes, W., Dothager, M., Lee, P. C., Wong, J., Xiong, D. D., et al. (2015) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.015966 · Cited by 93
Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis
Asaf, S., Khan, A. L., Khan, M. A., Waqas, M., Kang, ⋅.-M., Yun, B., & Lee, I. (2017) · Scientific Reports · doi:10.1038/s41598-017-07891-5 · Cited by 94
Resequencing of Common Bean Identifies Regions of Inter–Gene Pool Introgression and Provides Comprehensive Resources for Molecular Breeding
Lobaton, J. D., Miller, T. H., Gil, J., Ariza-Suárez, D., Hoz, J. D. L., Soler‐Garzón, A., Beebe, S. E., Duitama, J., Gepts, P., & Raatz, B. (2018) · The Plant Genome · doi:10.3835/plantgenome2017.08.0068 · Cited by 94
Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems
Denœud, F., Godfroy, O., Cruaud, C., Heesch, S., Nehr, Z., Tadrent, N., Couloux, A., Brillet-Guéguen, L., Delage, L., Mckeown, D., et al. (2024) · Cell · doi:10.1016/j.cell.2024.10.049 · Cited by 98
Description, Nomenclature, and Mapping of a Novel Cerebello-Renal Syndrome with the Molar Tooth Malformation
Valente, E. M., Salpietro, D. C., Brancati, F., Bertini, E., Galluccio, T., Tortorella, G., Briuglia, S., & Dallapiccola, B. (2003) · The American Journal of Human Genetics · doi:10.1086/378241 · Cited by 94
Microsatellite analysis reveals marked genetic differentiation between Haemonchus contortus laboratory isolates and provides a rapid system of genetic fingerprinting
Redman, E., Packard, E., Grillo, V., Smith, J. A., Jackson, F., & Gilleard, J. S. (2007) · International Journal for Parasitology · doi:10.1016/j.ijpara.2007.06.008 · Cited by 97

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
DOI: 10.1093/nar/27.2.573
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

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

Tandem repeats finder: a program to analyze DNA sequences

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks