ArticleMolecular ecology resources2019
DeviaTE: Assembly-free analysis and visualization of mobile genetic element composition.
Article in Molecular ecology resources, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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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Who cites it
29 citing papers in PubMed, 47 citations in OpenAlex.
- The ongoing invasion of the endogenous retrovirus Kuruka in natural Drosophila melanogaster populations.Nature communications · 2026Article
- Genome reshaping by Helitron transposons in Fusarium oxysporum TR4 affects secondary metabolism but not virulence.Nature communications · 2026Article
- The ongoing invasion of the endogenous retrovirusbioRxiv : the preprint server for biology · 2025Article
- Rapid emergence of non-autonomous elements may stop P-element invasions in the absence of a piRNA-based host defence.PLoS genetics · 2025Article
- Comparative genomics of the parasite Trichomonas vaginalis reveals genes involved in spillover from birds to humans.Nature communications · 2025Article
- Purifying selection shapes the dynamics of P-element invasion in Drosophila simulans populations.Genome biology · 2025Article
- Spatiotemporal Tracking of Three Novel Transposable Element Invasions in Drosophila melanogaster over the Last 30 Years.Molecular biology and evolution · 2025Article
- Exploring the Relationship of Transposable Elements and Ageing: Causes and Consequences.Genome biology and evolution · 2025Review
- On the origin of the P-element invasion in Drosophila simulans.Mobile DNA · 2025Article
- Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years.Nature communications · 2025Article
- GenomeDelta: detecting recent transposable element invasions without repeat library.Genome biology · 2024Article
- Experimentally evolvingGenome research · 2024Article
- Genomes of historical specimens reveal multiple invasions of LTR retrotransposons inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s.PLoS genetics · 2024Article
- Transposon Removal Reveals Their Adaptive Fitness Contribution.Genome biology and evolution · 2024Article
- The genomic distribution of transposable elements is driven by spatially variable purifying selection.Nucleic acids research · 2023Article
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.Mobile DNA · 2023Article
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.bioRxiv : the preprint server for biology · 2023Article
- Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Hybrid incompatibility between Drosophila virilis and D. lummei is stronger in the presence of transposable elements.Journal of evolutionary biology · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Transposable elements (TEs) are selfish DNA sequences that multiply within host genomes. They are present in most species investigated so far at varying degrees of abundance and sequence diversity. The TE composition may not only vary between but also within species and could have important biological implications. Variation in prevalence among populations may for example indicate a recent TE invasion, whereas sequence variation could indicate the presence of hyperactive or inactive forms. Gaining unbiased estimates of TE composition is thus vital for understanding the evolutionary dynamics of transposons. To this end, we developed DeviaTE, a tool to analyse and visualize TE abundance using Illumina or Sanger sequencing reads. Our tool requires sequencing reads of one or more samples (tissue, individual or population) and consensus sequences of TEs. It generates a table and a visual representation of TE composition. This allows for an intuitive assessment of coverage, sequence divergence, segregating SNPs and indels, as well as the presence of internal and terminal deletions. By contrasting the coverage between TEs and single copy genes, DeviaTE derives unbiased estimates of TE abundance. We show that naive approaches, which do not consider regions spanned by internal deletions, may substantially underestimate TE abundance. Using published data we demonstrate that DeviaTE can be used to study the TE composition within samples, identify clinal variation in TEs, compare TE diversity among species, and monitor TE invasions. Finally we present careful validations with publicly available and simulated data. DeviaTE is implemented in Python and distributed under the GPLv3 (https://github.com/W-L/deviaTE).
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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.