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Nucleic Acids Res. 2017 Jan 9;45(1):39-53. doi: 10.1093/nar/gkw1002. Epub 2016 Nov 28.

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences.

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Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy Los, Angeles, CA 90089, USA
Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA.
Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy Los, Angeles, CA 90089, USA.
Center for Computational Systems Biology, Fudan University, Shanghai 200433, China.


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 [Formula: see text] 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, [Formula: see text] 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 metagenomically-assembled marine SUP05 viruses and the human gut virus crAssphage, [Formula: see text]-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 [Formula: see text] ONF method will greatly improve the characterization of novel, metagenomic viruses.

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