PT  - JOURNAL ARTICLE
AU  - Tyler J. Dougan
AU  - Stephen R. Quake
TI  - Viral Taxonomy Derived From Evolutionary Genome Relationships
AID  - 10.1101/322511
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 322511
4099  - http://biorxiv.org/content/early/2018/05/15/322511.short
4100  - http://biorxiv.org/content/early/2018/05/15/322511.full
AB  - We describe a new genome alignment-based model for classification of viruses based on evolutionary genetic relationships. This approach uses information theory and a physical model to determine the information shared by the genes in two genomes. Pairwise comparisons of genes from the viruses are created from alignments using NCBI BLAST, and their match scores are combined to produce a metric between genomes, which is in turn used to determine a global classification using the 5,817 viruses on RefSeq. In cases where there is no measurable alignment between any genes, the method falls back to a coarser measure of genome relationship: the mutual information of k-mer frequency. This results in a principled model which depends only on the genome sequence, which captures many interesting relationships between viral families, and which creates clusters which correlate well with both the Baltimore and ICTV classifications. The incremental computational cost of classifying a novel virus is low and therefore newly discovered viruses can be quickly identified and classified.