ArticleBMC bioinformatics2018
MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- A highly contiguous chromosome-level genome assembly of the Chilean jack mackerel Trachurus murphyi.Scientific data · 2026Article
- Evolutionary Study of Transposable Elements: Structural Characterization and Phylogenomic Profiling in Plant Genomes.Journal of molecular evolution · 2026Review
- Haploid Mutation Mapping Identifies a Homoeologous Non-Reciprocal Translocation Linked to Reduced Fibre and Enhanced Protein in Brassica napus.Plant biotechnology journal · 2026Article
- First genome assemblies of Neotropical Thoracobombus bumblebees Bombus pauloensis and Bombus pullatus.G3 (Bethesda, Md.) · 2026Article
- Deciphering the dynamics of active autonomous terminal inverted repeat transposons in the plant kingdom.aBIOTECH · 2026Article
- Chromosome-level genome assembly of the deep-sea solemyid bivalve Acharax haimaensis.Scientific data · 2026Article
- Massive proliferation of retrotransposons contributes to genome size expansion in species of the Pseudocercospora genus.Mobile DNA · 2026Article
- Chromosome-level genome assembly of the alpine extremophyte Tibetan snow lotus, Saussurea hypsipeta Diels.Scientific data · 2026Article
- Plant MITEs: miniature transposable elements with major impacts.Mobile DNA · 2025Review
- MITE Annotation and Landscape in 207 Plant Genomes Reveal Their Evolutionary Dynamics and Functional Roles.Molecular ecology resources · 2025Article
- Community and functional stability in a working bioreactor degrading 1,4-dioxane at the Lowry Landfill Superfund Site.Applied and environmental microbiology · 2025Article
- Exploring the genomic landscape of mites and harnessing MITE insertion polymorphism markers in jute (Corchorus sp.).Scientific reports · 2025Article
- Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data:Journal of fungi (Basel, Switzerland) · 2025Article
- Conservative evolution of genetic and genomic features inbioRxiv : the preprint server for biology · 2025Article
- A Chromosome level assembly of pomegranate (Punica granatum L.) variety grown in arid environment.Scientific data · 2025Article
- Genomic and transcriptomic analyses of Heteropoda venatoria reveal the expansion of P450 family for starvation resistance in spiders.GigaScience · 2025Article
- Insect Phylogenomics: From Experiment Planning to Post-phylogenetic Analyses.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Unveiling host-parasite relationships through conserved MITEs in prokaryote and viral genomes.Nucleic acids research · 2024Article
- Discovery and genome-wide characterization of a novel miniature inverted repeat transposable element reveal genome-specific distribution in Glycine.Genes & genomics · 2024Article
- Haplotype-resolved and near-T2T genome assembly of the African catfish (Clarias gariepinus).Scientific data · 2024Article
23 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
backgroundMiniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify MITEs sequences.
resultsHere we describe MITE Tracker, a novel, open source software program that finds and classifies MITEs using an efficient alignment strategy to retrieve nearby inverted-repeat sequences from large genomes. This program groups them into high sequence homology families using a fast clustering algorithm and finally filters only those elements that were likely transposed from different genomic locations because of their low scoring flanking sequence alignment.
conclusionsMany programs have been proposed to find MITEs hidden in genomes. However, none of them are able to process large-scale genomes such as that of bread wheat. Furthermore, in many cases the existing methods perform high false-positive rates (or miss rates). The rice genome was used as reference to compare MITE Tracker against known tools. Our method turned out to be the most reliable in our tests. Indeed, it revealed more known elements, presented the lowest false-positive number and was the only program able to run with the bread wheat genome as input. In wheat, MITE Tracker discovered 6013 MITE families and allowed the first structural exploration of MITEs in the complete bread wheat genome.
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