Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life
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 traine...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-02-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-28965-7 |
| _version_ | 1811165971546636288 |
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| author | Logan Hallee Bohdan B. Khomtchouk |
| author_facet | Logan Hallee Bohdan B. Khomtchouk |
| author_sort | Logan Hallee |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-10T15:44:50Z |
| format | Article |
| id | doaj.art-fd3fb3e673384f4bb048337f1b230de7 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-10T15:44:50Z |
| publishDate | 2023-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-fd3fb3e673384f4bb048337f1b230de72023-02-12T12:12:29ZengNature PortfolioScientific Reports2045-23222023-02-0113111410.1038/s41598-023-28965-7Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of lifeLogan Hallee0Bohdan B. Khomtchouk1Center for Bioinformatics and Computational Biology, University of DelawareDepartment of BioHealth Informatics, Center for Computational Biology and Bioinformatics, Indiana UniversityAbstract 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.https://doi.org/10.1038/s41598-023-28965-7 |
| spellingShingle | Logan Hallee Bohdan B. Khomtchouk Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life Scientific Reports |
| title | Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life |
| title_full | Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life |
| title_fullStr | Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life |
| title_full_unstemmed | Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life |
| title_short | Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life |
| title_sort | machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life |
| url | https://doi.org/10.1038/s41598-023-28965-7 |
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