ArticleNature communications2025
TEtrimmer: a tool to automate the manual curation of transposable elements.
Article in Nature communications, 2025. 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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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed.
- From neuropeptides to toxins: illuminating the origins of venom complexity in cone snails.Molecular biology and evolution · 2026Article
- The 3D genome of Gigaspora margarita unveils stable chromatin and nucleolar organization and symbiont-dependent genome dynamics.The New phytologist · 2026Article
- Transposable elements in the era of data science EMBO course: a call for open, accessible, and collaborative TE resources.Mobile DNA · 2026Article
- Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtailbioRxiv : the preprint server for biology · 2026Article
- Biological Implications of a Detailed Repeat Annotation in Octopus vulgaris.Genome biology and evolution · 2026Article
- Ancient origin and dynamic evolution of bivalent spider toxins.Molecular biology and evolution · 2026Article
- Chromosome-level genome assembly of the sponge Halisarca dujardinii.Scientific data · 2026Article
- ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements.Mobile DNA · 2025Article
- Chromosome-level assembly of the club-legged grasshopper (Gomphocerus sibiricus) genome.G3 (Bethesda, Md.) · 2025Article
- Saprotrophic Arachnopeziza Species as New Resources to Study the Obligate Biotrophic Lifestyle of Powdery Mildew Fungi.Molecular ecology resources · 2025Article
- Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens.bioRxiv : the preprint server for biology · 2025Article
- Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals.Genome biology · 2025Article
- Comparative analysis of the mobilome yields new insights into its diversity, dynamics and evolution in parasites of the Trypanosomatidae family.Parasitology · 2025Article
- Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System.Molecular biology and evolution · 2025Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Transposable elements (TEs) are repetitive DNA sequences that move within genomes and play important roles in gene regulation and genome evolution. Accurate TE annotation in genomes is crucial for downstream analyses but challenging due to their sequence diversity and frequent fragmentation, including the occurrence of nested copies. We here present TEtrimmer, a tool that automates and replaces key steps of traditional manual curation of TEs. TEtrimmer combines phylogenetic tree analysis with the machine learning method DBSCAN to cluster TE sequences accurately and applies a sliding-window strategy to remove poorly conserved regions of TE-derived multiple sequence alignments. TEtrimmer also provides detailed report plots and features a graphical user interface (GUI) application. Tested on the genomes of six organisms belonging to various kingdoms of eukaryotic life and three simulated genomes, TEtrimmer consistently improved the identification of intact TEs compared to the established tools EDTA and RepeatModeler2.
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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.