ArticleBioinformatics (Oxford, England)2023
Decomposing mosaic tandem repeats accurately from long reads.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 12 citations in OpenAlex.
- ECHO: a nanopore sequencing-based workflow for (epi)genetic profiling of the human repeatome.Bioinformatics (Oxford, England) · 2026Article
- Enabling efficient and robust analysis of tandem repeats in genomic data using Wavefront-based String Decomposer.Genome research · 2026Article
- Transposable Element-Driven Genomic Plasticity: Unveiling the Evolutionary Mechanisms of Lifestyle Transition and Ecological Adaptation in Endophytic Fungi.Journal of fungi (Basel, Switzerland) · 2026Article
- The continued promise of genomic technologies and software in neurogenetics.Journal of neuromuscular diseases · 2025Review
- Multisample motif discovery and visualization for tandem repeats.Genome research · 2025Article
- Approximating edit distances between complex tandem repeats efficiently.Bioinformatics (Oxford, England) · 2025Article
- Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing.Nucleic acids research · 2025Article
- Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT andGenome research · 2024Article
- A landscape of complex tandem repeats within individual human genomes.Nature communications · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationOver the past 30 years, extended tandem repeats (TRs) have been correlated with ∼60 diseases with high odds ratios, and most known TRs consist of single repeat units. However, in the last few years, mosaic TRs composed of different units have been found to be associated with several brain disorders by long-read sequencing techniques. Mosaic TRs are difficult-to-characterize sequence configurations that are usually confirmed by manual inspection. Widely used tools are not designed to solve the mosaic TR problem and often fail to properly decompose mosaic TRs.
resultsWe propose an efficient algorithm that can decompose mosaic TRs in the input string with high sensitivity. Using synthetic benchmark data, we demonstrate that our program named uTR outperforms TRF and RepeatMasker in terms of prediction accuracy, this is especially true when mosaic TRs are more complex, and uTR is faster than TRF and RepeatMasker in most cases. AVAILABILITY AND IMPLEMENTATION: The software program uTR that implements the proposed algorithm is available at https://github.com/morisUtokyo/uTR.
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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.