ArticleBioinformatics (Oxford, England)2019
Dot2dot: accurate whole-genome tandem repeats discovery.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 22 citations in OpenAlex.
- Defining a tandem repeat catalog and variation clusters for genome-wide analyses.bioRxiv : the preprint server for biology · 2026Article
- Computational tools for tandem repeat detection using long-read sequencing.Briefings in bioinformatics · 2026Review
- Structure and evolution of the Forsythieae genome elucidated by chromosome-level genome comparison of Abeliophyllum distichum and Forsythia ovata (Oleaceae).Communications biology · 2025Article
- Bioinformatics for the Structural Genomics of Poxviruses.Methods in molecular biology (Clifton, N.J.) · 2025Article
- What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools.Frontiers in genetics · 2024Review
- USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences.BMC bioinformatics · 2022Article
- Revisiting tandem repeats in psychiatric disorders from perspectives of genetics, physiology, and brain evolution.Molecular psychiatry · 2022Review
- Finding long tandem repeats in long noisy reads.Bioinformatics (Oxford, England) · 2021Article
- BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data.Frontiers in big data · 2021Article
- Chloroplast Genome Sequencing, Comparative Analysis, and Discovery of Unique Cytoplasmic Variants in Pomegranate (Frontiers in genetics · 2021Article
- Review
- Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations.International journal of molecular sciences · 2020Article
- Long-read sequencing reveals a 4.4 kb tandem repeat region in the mitogenome of Echinococcus granulosus (sensu stricto) genotype G1.Parasites & vectors · 2019Article
- ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation.BMC genomics · 2019Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationLarge-scale sequencing projects have confirmed the hypothesis that eukaryotic DNA is rich in repetitions whose functional role needs to be elucidated. In particular, tandem repeats (TRs) (i.e. short, almost identical sequences that lie adjacent to each other) have been associated to many cellular processes and, indeed, are also involved in several genetic disorders. The need of comprehensive lists of TRs for association studies and the absence of a computational model able to capture their variability have revived research on discovery algorithms.
resultsBuilding upon the idea that sequence similarities can be easily displayed using graphical methods, we formalized the structure that TRs induce in dot-plot matrices where a sequence is compared with itself. Leveraging on the observation that a compact representation of these matrices can be built and searched in linear time, we developed Dot2dot: an accurate algorithm fast enough to be suitable for whole-genome discovery of TRs. Experiments on five manually curated collections of TRs have shown that Dot2dot is more accurate than other established methods, and completes the analysis of the biggest known reference genome in about one day on a standard PC. AVAILABILITY AND IMPLEMENTATION: Source code and datasets are freely available upon paper acceptance at the URL: https://github.com/Gege7177/Dot2dot. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.