ArticleNucleic acids research2012
Repeat or not repeat?--Statistical validation of tandem repeat prediction in genomic sequences.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
30 citing papers in PubMed.
- Pan-SSR architecture in Acrossocheilus fasciatus links cross-assembly repeat conservation, repeat-unit count variation, and genomic context.Molecular genetics and genomics : MGG · 2026Article
- pLM-Repeat: Exploiting the sequence representations of protein language models for sensitive repeat detection.Protein science : a publication of the Protein Society · 2026Article
- Accurate detection of tandem repeats exposes ubiquitous reuse of biological sequences.Nucleic acids research · 2025Article
- Tandem Repeats Provide Evidence for Convergent Evolution to Similar Protein Structures.Genome biology and evolution · 2025Article
- Discovery and Analysis of Repeat and Low-Complexity Architectures in Proteins and Their Conserved Evolutionary Relationships Using Self-Homology Dot Plots.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Evolutionary model of repeat insertions in Ataxin-3 traces the origin of the polyglutamine stretch to an ancestral ubiquitin binding module.Protein science : a publication of the Protein Society · 2024Article
- A novel hypervariable variable number tandem repeat in the dopamine transporter gene (Life science alliance · 2023Article
- Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species.Journal of evolutionary biology · 2023Review
- Whole Genome Sequencing Analysis of Effects of CRISPR/Cas9 inJournal of fungi (Basel, Switzerland) · 2022Article
- The Repeating, Modular Architecture of the HtrA Proteases.Biomolecules · 2022Article
- Identification of RareInternational journal of molecular sciences · 2021Article
- The Effect of Mutations in the TPR and Ankyrin Families of Alpha Solenoid Repeat Proteins.Frontiers in bioinformatics · 2021Review
- Beyond Microsatellite Instability: Intrinsic Disorder as a Potential Link Between Protein Short Tandem Repeats and Cancer.Frontiers in bioinformatics · 2021Article
- TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner.Frontiers in bioinformatics · 2021Article
- Self-analysis of repeat proteins reveals evolutionarily conserved patterns.BMC bioinformatics · 2020Article
- Article
- Accuracy of short tandem repeats genotyping tools in whole exome sequencing data.F1000Research · 2020Article
- Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.Nucleic acids research · 2019Review
- RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins.Nucleic acids research · 2018Article
- TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tandem repeats (TRs) represent one of the most prevalent features of genomic sequences. Due to their abundance and functional significance, a plethora of detection tools has been devised over the last two decades. Despite the longstanding interest, TR detection is still not resolved. Our large-scale tests reveal that current detectors produce different, often nonoverlapping inferences, reflecting characteristics of the underlying algorithms rather than the true distribution of TRs in genomic data. Our simulations show that the power of detecting TRs depends on the degree of their divergence, and repeat characteristics such as the length of the minimal repeat unit and their number in tandem. To reconcile the diverse predictions of current algorithms, we propose and evaluate several statistical criteria for measuring the quality of predicted repeat units. In particular, we propose a model-based phylogenetic classifier, entailing a maximum-likelihood estimation of the repeat divergence. Applied in conjunction with the state of the art detectors, our statistical classification scheme for inferred repeats allows to filter out false-positive predictions. Since different algorithms appear to specialize at predicting TRs with certain properties, we advise applying multiple detectors with subsequent filtering to obtain the most complete set of genuine repeats.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.