ArticleGenes2021
InpactorDB: A Classified Lineage-Level Plant LTR Retrotransposon Reference Library for Free-Alignment Methods Based on Machine Learning.
Article in Genes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 22 citations in OpenAlex.
- DANTE and DANTE_LTR: lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes.NAR genomics and bioinformatics · 2024Article
- The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California.G3 (Bethesda, Md.) · 2024Article
- Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology.Evolutionary applications · 2024Article
- Lineage-specific amplification and epigenetic regulation of LTR-retrotransposons contribute to the structure, evolution, and function of Fabaceae species.BMC genomics · 2023Article
- Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes.Briefings in bioinformatics · 2023Article
- InpactorDB: A Plant LTR Retrotransposon Reference Library.Methods in molecular biology (Clifton, N.J.) · 2023Article
- PlantLTRdb: An interactive database for 195 plant species LTR-retrotransposons.Frontiers in plant science · 2023Article
- Article
- Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain.Plant physiology · 2022Article
- Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species.International journal of molecular sciences · 2022Article
- Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning.Journal of integrative bioinformatics · 2022Article
- Article
- An Atlas of Plant Transposable Elements.F1000Research · 2021Article
- Efficient homology-based annotation of transposable elements using minimizers.Applications in plant sciencesArticle
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long terminal repeat (LTR) retrotransposons are mobile elements that constitute the major fraction of most plant genomes. The identification and annotation of these elements via bioinformatics approaches represent a major challenge in the era of massive plant genome sequencing. In addition to their involvement in genome size variation, LTR retrotransposons are also associated with the function and structure of different chromosomal regions and can alter the function of coding regions, among others. Several sequence databases of plant LTR retrotransposons are available for public access, such as PGSB and RepetDB, or restricted access such as Repbase. Although these databases are useful to identify LTR-RTs in new genomes by similarity, the elements of these databases are not fully classified to the lineage (also called family) level. Here, we present InpactorDB, a semi-curated dataset composed of 130,439 elements from 195 plant genomes (belonging to 108 plant species) classified to the lineage level. This dataset has been used to train two deep neural networks (i.e., one fully connected and one convolutional) for the rapid classification of these elements. In lineage-level classification approaches, we obtain up to 98% performance, indicated by the F1-score, precision and recall scores.
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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 Socratic graph.