ArticleGenes2021
DARTS: An Algorithm for Domain-Associated Retrotransposon Search in Genome Assemblies.
Article in Genes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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.
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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
7 citing papers in PubMed.
- Evolution ofPlants (Basel, Switzerland) · 2026Article
- Heat-induced transcriptional activation of LTR retrotransposons in the regenerative flatworm Macrostomum lignano.Mobile DNA · 2025Article
- Origin and Evolution of Plant Long Terminal Repeat Retrotransposons with Additional Ribonuclease H.Genome biology and evolution · 2023Article
- Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on body plan evolution and photosymbiosis.G3 (Bethesda, Md.) · 2023Article
- MegaLTR: a web server and standalone pipeline for detecting and annotating LTR-retrotransposons in plant genomes.Frontiers in plant science · 2023Article
- An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Methodologies for theGenes · 2022Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Retrotransposons comprise a substantial fraction of eukaryotic genomes, reaching the highest proportions in plants. Therefore, identification and annotation of retrotransposons is an important task in studying the regulation and evolution of plant genomes. The majority of computational tools for mining transposable elements (TEs) are designed for subsequent genome repeat masking, often leaving aside the element lineage classification and its protein domain composition. Additionally, studies focused on the diversity and evolution of a particular group of retrotransposons often require substantial customization efforts from researchers to adapt existing software to their needs. Here, we developed a computational pipeline to mine sequences of protein-coding retrotransposons based on the sequences of their conserved protein domains-DARTS (Domain-Associated Retrotransposon Search). Using the most abundant group of TEs in plants-long terminal repeat (LTR) retrotransposons (LTR-RTs)-we show that DARTS has radically higher sensitivity for LTR-RT identification compared to the widely accepted tool LTRharvest. DARTS can be easily customized for specific user needs. As a result, DARTS returns a set of structurally annotated nucleotide and amino acid sequences which can be readily used in subsequent comparative and phylogenetic analyses. DARTS may facilitate researchers interested in the discovery and detailed analysis of the diversity and evolution of retrotransposons, LTR-RTs, and other protein-coding TEs.
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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.