ArticleNucleic acids research2015
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Review
- Complex determinants of R-loop formation at transposable elements and major DNA satellites.Genetics · 2025Article
- Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.Plant biotechnology journal · 2025Article
- Transposable Element (TE) insertion predictions from RNAseq inputs and TE impact on RNA splicing and gene expression in Drosophila brain transcriptomes.Mobile DNA · 2024Article
- TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.Genome biology · 2023Article
- Effects of Wolbachia on Transposable Element Expression Vary Between Drosophila melanogaster Host Genotypes.Genome biology and evolution · 2023Article
- Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line.Nucleic acids research · 2022Article
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila.Genome biology · 2021Article
- Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster.Molecular ecology · 2021Article
- Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses.Molecular biology and evolution · 2020Article
- Article
- TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data.Nucleic acids research · 2020Article
- Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding.Molecular biology reports · 2020Review
- T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data.Bioinformatics (Oxford, England) · 2020Article
- Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster.Nucleic acids research · 2020Article
- Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster.Nucleic acids research · 2019Article
- On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements.Genes · 2019Review
- Population-specific dynamics and selection patterns of transposable element insertions in European natural populations.Molecular ecology · 2019Article
- Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila.PLoS genetics · 2019Article
Corrections and comments
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4 authors.
Funding
Abstract
Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a broadly applicable and flexible tool: T-lex2. T-lex2 is the only available software that allows routine, automatic and accurate genotyping of individual TE insertions and estimation of their population frequencies both using individual strain and pooled next-generation sequencing data. Furthermore, T-lex2 also assesses the quality of the calls allowing the identification of miss-annotated TEs and providing the necessary information to re-annotate them. The flexible and customizable design of T-lex2 allows running it in any genome and for any type of TE insertion. Here, we tested the fidelity of T-lex2 using the fly and human genomes. Overall, T-lex2 represents a significant improvement in our ability to analyze the contribution of TEs to genome function and evolution as well as learning about the biology of TEs. T-lex2 is freely available online at http://sourceforge.net/projects/tlex.
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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.