ampir: an R package for fast genome-wide prediction of antimicrobial peptides

Fingerhut, Legana C. H. W., Miller, David J., Strugnell, Jan M., Daly, Norelle L., and Cooke, Ira R. (2020) ampir: an R package for fast genome-wide prediction of antimicrobial peptides. Bioinformatics, 36 (21). btaa653.

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Abstract

Antimicrobial peptides (AMPs) are the 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 implementation ampir 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.

Item ID: 64750
Item Type: Article (Research - C1)
ISSN: 1367-4811
Copyright Information: © The Author(s) 2020. Published by Oxford University Press. All rights reserved.
Funders: James Cook University
Date Deposited: 29 Oct 2020 05:40
FoR Codes: 31 BIOLOGICAL SCIENCES > 3101 Biochemistry and cell biology > 310109 Proteomics and intermolecular interactions (excl. medical proteomics) @ 100%
SEO Codes: 92 HEALTH > 9299 Other Health > 929999 Health not elsewhere classified @ 100%
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