Recent advances in metagenomics provided a valuable alternative to culture-based approaches for better sampling viral diversity. However, some of newly identified viruses lack sequence similarity to any of previously sequenced ones, and cannot be easily assigned to their hosts. Here we present a bioinformatic approach to this problem. We developed classifiers capable of distinguishing eukaryotic viruses from the phages achieving almost 95% prediction accuracy. The classifiers are wrapped in Host Taxon Predictor (HTP) software written in Python which is freely available at https://github.com/wojciech-galan/viruses_classifier . HTP's performance was later demonstrated on a collection of newly identified viral genomes and genome fragments. In summary, HTP is a culture- and alignment-free approach for distinction between phages and eukaryotic viruses. We have also shown that it is possible to further extend our method to go up the evolutionary tree and predict whether a virus can infect narrower taxa.
Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses
Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences
Novel positive-sense, single-stranded RNA (+ssRNA) virus with di-cistronic genome from intestinal content of freshwater carp (Cyprinus carpio)
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies
Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging
External validation of two prediction models identifying employees at risk of high sickness absence: cohort study with 1-year follow-up
Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses
Virus isolate from carp: genetic characterization reveals a novel picornavirus with two aphthovirus 2A-like sequences
Genome analysis of a novel, highly divergent picornavirus from common kestrel (Falco tinnunculus): the first non-enteroviral picornavirus with type-I-like IRES
Novel approach for identification of influenza virus host range and zoonotic transmissible sequences by determination of host-related associative positions in viral genome segments
Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
Highly diverse population of Picornaviridae and other members of the Picornavirales, in Cameroonian fruit bats
Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code
Comparative studies of alignment, alignment-free and SVM based approaches for predicting the hosts of viruses based on viral sequences
VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families.
Bacteriophage: Phage Therapy
Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.