Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life
Date
2023-02-06
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Scientific Reports
Abstract
In this study, we investigate how an organism’s codon usage bias can serve as a predictor and classifier of various genomic and evolutionary traits across the domains of life. We perform secondary analysis of existing genetic datasets to build several AI/machine learning models. When trained on codon usage patterns of nearly 13,000 organisms, our models accurately predict the organelle of origin and taxonomic identity of nucleotide samples. We extend our analysis to identify the most influential codons for phylogenetic prediction with a custom feature ranking ensemble. Our results suggest that the genetic code can be utilized to train accurate classifiers of taxonomic and phylogenetic features. We then apply this classification framework to open reading frame (ORF) detection. Our statistical model assesses all possible ORFs in a nucleotide sample and rejects or deems them plausible based on the codon usage distribution. Our dataset and analyses are made publicly available on GitHub and the UCI ML Repository to facilitate open-source reproducibility and community engagement.
Description
© The Author(s) 2023. This article was originally published in Scientific Reports. The version of record is available at: https://doi.org/10.1038/s41598-023-28965-7.
Keywords
computational biology and bioinformatics, genome informatics, machine learning
Citation
Hallee, L., Khomtchouk, B.B. Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life. Sci Rep 13, 2088 (2023). https://doi.org/10.1038/s41598-023-28965-7