A viral proteomic tree server and its application to a marine metagenomic study
1Institute for Chemical Research, Kyoto University, 2Graduate School of Agriculture, Kyoto University, 3Aix Marseille Universit_, CNRS, IGS UMR 7256, Marseille, France
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.
keywords:virus,comparative genomics,web server,metagenome