ArticleBioinformatics (Oxford, England)2020
The string decomposition problem and its applications to centromere analysis and assembly.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
- Hunting for microsatellite instability in long-read data with Owl.PLoS computational biology · 2026Article
- Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes.Genome research · 2026Article
- Article
- Complete chromosome 21 centromere sequencing of families with Down syndrome.American journal of human genetics · 2026Article
- Enabling efficient and robust analysis of tandem repeats in genomic data using Wavefront-based String Decomposer.Genome research · 2026Article
- Higher order repeat structures reflect diverging evolutionary paths in maize centromeres and knobs.Genome biology · 2026Article
- mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing.Bioinformatics (Oxford, England) · 2026Article
- A global view of human centromere variation and evolution.bioRxiv : the preprint server for biology · 2025Article
- Hybridization Drives Trait Integration in Telomere-To-Telomere Apocynum Genomes.Plant biotechnology journal · 2025Article
- Complete chromosome 21 centromere sequencing of families with Down syndrome reveals centromere size asymmetry.bioRxiv : the preprint server for biology · 2025Article
- Telomere-to-telomere gapless genome assembly of Triplophysa yaopeizhii.Scientific data · 2025Article
- Approximating edit distances between complex tandem repeats efficiently.Bioinformatics (Oxford, England) · 2025Article
- Centromere Landscapes Resolved from Hundreds of Human Genomes.Genomics, proteomics & bioinformatics · 2024Article
- The centromere landscapes of four karyotypically diverse Papaver species provide insights into chromosome evolution and speciation.Cell genomics · 2024Article
- Article
- Efficient genome monomer higher-order structure annotation and identification using the GRMhor algorithm.Bioinformatics advances · 2024Article
- Advances in the discovery and analyses of human tandem repeats.Emerging topics in life sciences · 2023Review
- A landscape of complex tandem repeats within individual human genomes.Nature communications · 2023Article
- Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv.Nucleic acids research · 2023Article
- quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification.Horticulture research · 2023Article
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3 authors.
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Abstract
motivationRecent attempts to assemble extra-long tandem repeats (such as centromeres) faced the challenge of translating long error-prone reads from the nucleotide alphabet into the alphabet of repeat units. Human centromeres represent a particularly complex type of high-order repeats (HORs) formed by chromosome-specific monomers. Given a set of all human monomers, translating a read from a centromere into the monomer alphabet is modeled as the String Decomposition Problem. The accurate translation of reads into the monomer alphabet turns the notoriously difficult problem of assembling centromeres from reads (in the nucleotide alphabet) into a more tractable problem of assembling centromeres from translated reads.
resultsWe describe a StringDecomposer (SD) algorithm for solving this problem, benchmark it on the set of long error-prone Oxford Nanopore reads generated by the Telomere-to-Telomere consortium and identify a novel (rare) monomer that extends the set of known X-chromosome specific monomers. Our identification of a novel monomer emphasizes the importance of identification of all (even rare) monomers for future centromere assembly efforts and evolutionary studies. To further analyze novel monomers, we applied SD to the set of recently generated long accurate Pacific Biosciences HiFi reads. This analysis revealed that the set of known human monomers and HORs remains incomplete. SD opens a possibility to generate a complete set of human monomers and HORs for using in the ongoing efforts to generate the complete assembly of the human genome. AVAILABILITY AND IMPLEMENTATION: StringDecomposer is publicly available on https://github.com/ablab/stringdecomposer. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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