ArticleBriefings in bioinformatics2023
Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Harnessing artificial intelligence in plant breeding: innovations in digital phenotyping and breeding methodologies.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- A chromosome-level genome assembly of Vanilla planifolia uncovers the genomic architecture underlying partial endoreplication.BMC genomics · 2026Article
- panHiTE: A comprehensive and accurate pipeline for TE detection in large-scale population genomes.Plant communications · 2026Article
- Article
- Transformer-Based Classification of Transposable Element Consensus Sequences with TEclass2.Biology · 2025Article
- CREATE: a novel attention-based framework for efficient classification of transposable elements.Briefings in bioinformatics · 2025Article
- DANTE and DANTE_LTR: lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes.NAR genomics and bioinformatics · 2024Article
- De novo genome assembly of white clover (Trifolium repens L.) reveals the role of copy number variation in rapid environmental adaptation.BMC biology · 2024Article
- Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats.Mobile DNA · 2024Article
- The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.Nature genetics · 2024Article
- From tradition to innovation: conventional and deep learning frameworks in genome annotation.Briefings in bioinformatics · 2024Review
- Selection signatures and population dynamics of transposable elements in lima bean.Communications biology · 2023Article
- MegaLTR: a web server and standalone pipeline for detecting and annotating LTR-retrotransposons in plant genomes.Frontiers in plant science · 2023Article
- Article
- Efficient homology-based annotation of transposable elements using minimizers.Applications in plant sciencesArticle
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Authors and funding
9 authors.
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Abstract
LTR-retrotransposons are the most abundant repeat sequences in plant genomes and play an important role in evolution and biodiversity. Their characterization is of great importance to understand their dynamics. However, the identification and classification of these elements remains a challenge today. Moreover, current software can be relatively slow (from hours to days), sometimes involve a lot of manual work and do not reach satisfactory levels in terms of precision and sensitivity. Here we present Inpactor2, an accurate and fast application that creates LTR-retrotransposon reference libraries in a very short time. Inpactor2 takes an assembled genome as input and follows a hybrid approach (deep learning and structure-based) to detect elements, filter partial sequences and finally classify intact sequences into superfamilies and, as very few tools do, into lineages. This tool takes advantage of multi-core and GPU architectures to decrease execution times. Using the rice genome, Inpactor2 showed a run time of 5 minutes (faster than other tools) and has the best accuracy and F1-Score of the tools tested here, also having the second best accuracy and specificity only surpassed by EDTA, but achieving 28% higher sensitivity. For large genomes, Inpactor2 is up to seven times faster than other available bioinformatics tools.
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