rAMPage: Rapid Antimicrobial Peptide Annotation and Gene Estimation
Date:
Abstract: Antimicrobial peptides (AMPs) are a family of short defence proteins produced naturally by all organisms. Since AMPs do not confer resistance as easily as antibiotics, they are a potential alternative to antibiotics. Past research has shown that amphibians have the richest known AMP diversity, specifically the North American bullfrog has demonstrated potential in aiding the discovery of novel putative AMPs. Antibiotic resistance is becoming more prevalent each day, requiring agricultural practices to reduce the use of antibiotics to protect human health, animal health, and food safety. rAMPage is a scalable bioinformatics-based discovery platform for mining AMP sequences in publicly available genomic resources. RNA-seq amphibian and insect reads from the Sequence Read Archive (SRA) are used. After trimming, reads are assembled with RNA-Bloom into transcripts, filtered, and translated in silico. Then, the translated protein sequences are compared to known AMP sequences from the NCBI protein database and specific AMP databases, via homology search. These sequences are cleaved into their mature/bioactive form. Next, machine learning algorithm AMPlify, is employed to classify and prioritize the candidate AMPs based on their AMP probability score. Finally, these candidate AMPs are annotated and characterized. Across 84 datasets, rAMPage detected >1000 putative AMPs for downstream validation.
Click here to view the poster presented at ISMB/ECCB 2021 in the General Computational Biology COSI.
Lin, D., Nip, K. M., Aninta, S. I., Li, C., Warren, R. L., Helbing, C., Hoang, L., & Birol, I. (2021). “rAMPage: Rapid Antimicrobial Peptide Annotation and Gene Estimation.” Intelligent Systems For Molecular Biology (ISMB)/European Conference On Computational Biology (ECCB). https://www.iscb.org/ismbeccb2021