ampir: an R package for fast genome-wide prediction of antimicrobial peptides
ampir: an R package for fast genome-wide prediction of antimicrobial peptides
Abstract SummaryAntimicrobial peptides (AMPs) are key components of the innate immune system that protect against pathogens, regulate the microbiome, and are promising targets for pharmaceutical research. Computational tools based on machine learning have the potential to aid discovery of genes encoding novel AMPs but existing approaches are not designed for genome-wide scans. To facilitate such genome-wide discovery of AMPs we developed a fast and accurate AMP classification framework, ampir. ampir is designed for high throughput, integrates well with existing bioinformatics pipelines, and has much higher classification accuracy than existing methods when applied to whole genome data. Availability and Implementationampir is implemented primarily in R with core feature calculation methods written in C++. Release versions are available via CRAN and work on all major operating systems. The development version is maintained at https://github.com/legana/ampir Contactlegana.fingerhut@my.jcu.edu.au; ira.cooke@jcu.edu.au Supplementary informationSupplementary data are available at https://github.com/legana/amp_pub
Strugnell Jan M.、Fingerhut Legana C.H.W、Miller David J.、Cooke Ira R.、Daly Norelle L.
Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook UniversityCentre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University||Department of Molecular and Cell Biology, James Cook University||ARC Centre of Excellence for Coral Reef Studies, Australian National UniversityCentre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University||Department of Molecular and Cell Biology, James Cook University||ARC Centre of Excellence for Coral Reef Studies, Australian National UniversityCentre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University||Department of Molecular and Cell Biology, James Cook UniversityCentre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University||Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University
生物科学研究方法、生物科学研究技术计算技术、计算机技术生物科学现状、生物科学发展
Strugnell Jan M.,Fingerhut Legana C.H.W,Miller David J.,Cooke Ira R.,Daly Norelle L..ampir: an R package for fast genome-wide prediction of antimicrobial peptides[EB/OL].(2025-03-28)[2025-05-21].https://www.biorxiv.org/content/10.1101/2020.05.07.082412.点此复制
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