Biology
Document Type
Article
Abstract
Viruses and their host genomes often share similar oligonucleotide frequency (ONF) patterns, which can be used to predict the host of a given virus by finding the host with the greatest ONF similarity. We comprehensively compared 11 ONF metrics using several k-mer lengths for predicting host taxonomy from among ∼32 000 prokaryotic genomes for 1427 virus isolate genomes whose true hosts are known. The background-subtracting measure d2 ∗ at k = 6 gave the highest host prediction accuracy (33%, genus level) with reasonable computational times. Requiring a maximum dissimilarity score for making predictions (thresholding) and taking the consensus of the 30 most similar hosts further improved accuracy. Using a previous dataset of 820 bacteriophage and 2699 bacterial genomes, d2 ∗ host prediction accuracies with thresholding and consensus methods (genus-level: 64%) exceeded previous Euclidian distance ONF (32%) or homology-based (22-62%) methods. When applied to metagenomicallyassembled marine SUP05 viruses and the human gut virus crAssphage, d2 ∗-based predictions overlapped (i.e. some same, some different) with the previously inferred hosts of these viruses. The extent of overlap improved when only using host genomes or metagenomic contigs from the same habitat or samples as the query viruses. The d2 ∗ ONF method will greatly improve the characterization of novel, metagenomic viruses.
Publication Title
Nucleic Acids Research
Publication Date
1-9-2017
Volume
45
Issue
1
First Page
39
Last Page
53
ISSN
0305-1048
DOI
10.1093/nar/gkw1002
Keywords
viruses, host genomes, oligonucleotide frequency
Repository Citation
Ahlgren, Nathan A.; Ren, Jie; Lu, Yang Young; Fuhrman, Jed A.; and Sun, Fengzhu, "Alignment-free d2∗ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences" (2017). Biology. 68.
https://commons.clarku.edu/faculty_biology/68
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright Conditions
Ahlgren, N. A., Ren, J., Lu, Y. Y., Fuhrman, J. A., & Sun, F. (2017). Alignment-free oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences. Nucleic acids research, 45(1), 39-53. https://doi.org/10.1093/nar/gkw1002
