ArticleBiology2018
Inpactor, Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons and Its Application for Pineapple LTR Retrotransposons Diversity and Dynamics.
Article in Biology, 2018. 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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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
14 citing papers in PubMed.
- The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.Nature genetics · 2024Article
- Review
- Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes.Briefings in bioinformatics · 2023Article
- Article
- InpactorDB: A Plant LTR Retrotransposon Reference Library.Methods in molecular biology (Clifton, N.J.) · 2023Article
- G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era.Evolutionary bioinformatics online · 2023Article
- Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower (Plants (Basel, Switzerland) · 2022Article
- Article
- TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets.Biology · 2020Article
- Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference inInternational journal of molecular sciences · 2020Article
- Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning.International journal of molecular sciences · 2019Review
- LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo.BMC genomics · 2019Article
- Article
- The apricot (Horticulture research · 2019Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One particular class of Transposable Elements (TEs), called Long Terminal Repeats (LTRs), retrotransposons, comprises the most abundant mobile elements in plant genomes. Their copy number can vary from several hundreds to up to a few million copies per genome, deeply affecting genome organization and function. The detailed classification of LTR retrotransposons is an essential step to precisely understand their effect at the genome level, but remains challenging in large-sized genomes, requiring the use of optimized bioinformatics tools that can take advantage of supercomputers. Here, we propose a new tool: Inpactor, a parallel and scalable pipeline designed to classify LTR retrotransposons, to identify autonomous and non-autonomous elements, to perform RT-based phylogenetic trees and to analyze their insertion times using High Performance Computing (HPC) techniques. Inpactor was tested on the classification and annotation of LTR retrotransposons in pineapple, a recently-sequenced genome. The pineapple genome assembly comprises 44% of transposable elements, of which 23% were classified as LTR retrotransposons. Exceptionally, 16.4% of the pineapple genome assembly corresponded to only one lineage of the
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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.