ArticleNucleic acids research2022
TransposonUltimate: software for transposon classification, annotation and detection.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed.
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- Evolutionary Study of Transposable Elements: Structural Characterization and Phylogenomic Profiling in Plant Genomes.Journal of molecular evolution · 2026Review
- First genome assemblies of Neotropical Thoracobombus bumblebees Bombus pauloensis and Bombus pullatus.G3 (Bethesda, Md.) · 2026Article
- Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific.The ISME journal · 2026Article
- Gene duplication, horizontal gene transfer, and trait trade-offs drive evolution of postfire resource acquisition in pyrophilous fungi.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A chromosome-level genome assembly and multi-omics analyses provide insights into the biosynthesis of piperlongumine in Piper sarmentosum.Communications biology · 2026Article
- Anuran genome size evolution is driven by relatively recent retrotransposon activity and by life history.BMC genomics · 2025Article
- Sex differentiation, divergence, and introgression in the leishmaniasis vectorbioRxiv : the preprint server for biology · 2025Article
- CREATE: a novel attention-based framework for efficient classification of transposable elements.Briefings in bioinformatics · 2025Article
- Artificial intelligence in cancer: applications, challenges, and future perspectives.Molecular cancer · 2025Review
- The inbred newt genome unveils molecular mechanisms of behavior, development, and regeneration in urodele amphibians.iScience · 2025Article
- Outcrossing Complicates Mutation Purging by Trapping Single Nucleotide Polymorphisms in Structural Variant Mutations.bioRxiv : the preprint server for biology · 2025Article
- Transposon Dynamics Drive Genome Evolution and Regulate Genetic Mechanisms of Agronomic Traits in Cotton.Plants (Basel, Switzerland) · 2025Article
- Genomic analysis of the zooplankton-associated pathogenic bacteriumMicrobial genomics · 2025Article
- Transposable elements and heterochromatic regions are enriched for structural variation and sequence divergence in the genome of wild-type Caenorhabditis elegans.G3 (Bethesda, Md.) · 2025Article
- Conservative evolution of genetic and genomic features inbioRxiv : the preprint server for biology · 2025Article
- Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress.Nature communications · 2025Article
- Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.Plant biotechnology journal · 2025Article
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4 authors.
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Abstract
Most genomes harbor a large number of transposons, and they play an important role in evolution and gene regulation. They are also of interest to clinicians as they are involved in several diseases, including cancer and neurodegeneration. Although several methods for transposon identification are available, they are often highly specialised towards specific tasks or classes of transposons, and they lack common standards such as a unified taxonomy scheme and output file format. We present TransposonUltimate, a powerful bundle of three modules for transposon classification, annotation, and detection of transposition events. TransposonUltimate comes as a Conda package under the GPL-3.0 licence, is well documented and it is easy to install through https://github.com/DerKevinRiehl/TransposonUltimate. We benchmark the classification module on the large TransposonDB covering 891,051 sequences to demonstrate that it outperforms the currently best existing solutions. The annotation and detection modules combine sixteen existing softwares, and we illustrate its use by annotating Caenorhabditis elegans, Rhizophagus irregularis and Oryza sativa subs. japonica genomes. Finally, we use the detection module to discover 29 554 transposition events in the genomes of 20 wild type strains of C. elegans. Databases, assemblies, annotations and further findings can be downloaded from (https://doi.org/10.5281/zenodo.5518085).
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