ArticleBMC medical genomics2018
MiteFinderII: a novel tool to identify miniature inverted-repeat transposable elements hidden in eukaryotic genomes.
Article in BMC medical genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Biological Implications of a Detailed Repeat Annotation in Octopus vulgaris.Genome biology and evolution · 2026Article
- 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
- CREATE: a novel attention-based framework for efficient classification of transposable elements.Briefings in bioinformatics · 2025Article
- Conservative evolution of genetic and genomic features inbioRxiv : the preprint server for biology · 2025Article
- A chromosome-scale reference assembly of Vigna radiata enables delineation of centromeres and telomeres.Scientific data · 2025Article
- Repeat-induced point mutations driving Parastagonospora nodorum genomic diversity are balanced by selection against non-synonymous mutations.Communications biology · 2024Article
- Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats.Mobile DNA · 2024Article
- Review
- Chromosome-level genome assembly of the silver pomfret Pampus argenteus.Scientific data · 2024Article
- A chromosome-scale genome assembly of mungbean (PeerJ · 2024Article
- Review
- RepBox: a toolbox for the identification of repetitive elements.BMC bioinformatics · 2023Article
- Mitochondrial genome sequencing and analysis of the invasivebioRxiv : the preprint server for biology · 2023Article
- The identification of retro-DNAs in primate genomes as DNA transposons mobilizing via retrotransposition.F1000Research · 2023Article
- Article
- Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons.BMC genomics · 2022Article
- TransposonUltimate: software for transposon classification, annotation and detection.Nucleic acids research · 2022Article
- Methodologies for theGenes · 2022Review
- Characterization of B-Genome Specific High Copy hAT MITE Families inFrontiers in plant science · 2020Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMiniature inverted-repeat transposable element (MITE) is a type of class II non-autonomous transposable element playing a crucial role in the process of evolution in biology. There is an urgent need to develop bioinformatics tools to effectively identify MITEs on a whole genome-wide scale. However, most of currently existing tools suffer from low ability to deal with large eukaryotic genomes.
methodsIn this paper, we proposed a novel tool MiteFinderII, which was adapted from our previous algorithm MiteFinder, to efficiently detect MITEs from genomics sequences. It has six major steps: (1) build K-mer Index and search for inverted repeats; (2) filtration of inverted repeats with low complexity; (3) merger of inverted repeats; (4) filtration of candidates with low score; (5) selection of final MITE sequences; (6) selection of representative sequences.
resultsTo test the performance, MiteFinderII and three other existing algorithms were applied to identify MITEs on the whole genome of oryza sativa. Results suggest that MiteFinderII outperforms existing popular tools in terms of both specificity and recall. Additionally, it is much faster and more memory-efficient than other tools in the detection.
conclusionMiteFinderII is an accurate and effective tool to detect MITEs hidden in eukaryotic genomes. The source code is freely accessible at the website: https://github.com/screamer/miteFinder .
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