PH-106:

A viral proteomic tree server and its application to a marine metagenomic study

Viruses are pathogens of animals and plants, and they are also involved in the control of the dynamics of microbial ecosystems. Studies of viruses are thus important in different research domains including medical, agricultural and ecological sciences. Genomics has been a powerful tool to investigate viruses, and up to now over 4,500 viral genomes have been determined. Thanks to the recent advancements in sequence technologies, viral genomic data from both isolated viruses and environmental samples are expected to accumulate rapidly in the near future.
Viral genomics often involves the identification of phylogenetically related viruses. Reconstruction of gene phylogeny is a typical approach for this, but it sometimes faces difficulties when viral genomes in comparison do not share any conserved genes. An alternative approach is the construction of “viral proteomic trees”, which reveal the genome-wide sequence similarity relationships among viruses.
We have been developing a web-based service, VirPhy, for proteomic tree analyses of viral genomes. VirPhy is currently designed as follows. VirPhy takes viral genomes as a user input. It generates a proteomic tree based on tBLASTx scores between the query genomes and other previously sequenced viral genomes. The proteomic tree is visualized as a rectangular or circular dendrogram with the taxonomic information of the viruses and their known hosts. VirPhy provides dot-plot and multiple genomic alignment views to compare genomes that the users can dynamically select from the proteomic tree view. Proteomic trees, dot-plots, genomic alignments are drawn as vector images (SVG) generated by JavaScript, and can be easily edited by users. VirPhy also predicts genes in the query genomes and performs gene function annotation. Along with the functionalities of VirPhy, we will present the effectiveness of VirPhy with its application to the analysis of newly determined viral genomes that we obtained from marine virome projects.

keywords:virus,comparative genomics,web server,metagenome