ArticleMobile DNA2022
Software evaluation for de novo detection of transposons.
Article in Mobile DNA, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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.
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
21 citing papers in PubMed, 34 citations in OpenAlex.
- TE_Bench: a foundational benchmarking workflow for transposable element annotation pipelines.Mobile DNA · 2026Article
- Abscisic Acid Induces Triacylglycerol Accumulation and Lipid Remodelling in Chloroplast-Containing Green Tissues of Lemna minor.Plant, cell & environment · 2026Article
- A chromosome-level genome assembly of Cistanche deserticola provides insights into its evolution and molecular mechanisms of parasitism.Plant communications · 2026Article
- Transformer-Based Classification of Transposable Element Consensus Sequences with TEclass2.Biology · 2025Article
- ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements.Mobile DNA · 2025Article
- TEtrimmer: a tool to automate the manual curation of transposable elements.Nature communications · 2025Article
- Chromosome-level genome assembly and anticoagulant protein annotation of the buffalo leech Hirudinaria bpling (Hirudinea: Hirudinidae).BMC genomics · 2025Article
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- MCHelper automatically curates transposable element libraries across eukaryotic species.Genome research · 2024Article
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- Genome resequencing reveals the genetic basis of population evolution, local adaptation, and rewiring of the rhizome metabolome inHorticulture research · 2024Article
- HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation.Nature communications · 2024Article
- Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline.Molecular biology and evolution · 2024Article
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- AdvancingPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes acrossGenome research · 2023Article
- Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China.BMC genomic data · 2023Article
- Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes.Briefings in bioinformatics · 2023Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. As expected, tools that build TE-models performed better than k-mer counting ones, with RepeatModeler beating competitors in most datasets. However, there is a tendency for most tools to identify TE-regions in a fragmented manner and it is also frequent that small TEs or fragmented TEs are not detected. Consequently, the identification of TEs is still a challenging endeavor and it requires a significant manual curation by an experienced expert. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.
Identifiers
What OpenQuestion holds
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.