PhEVER: an innovative database
The major disadvantage of public phylogeny databases is their taxonomical compartmentalisation: they look for homologies either between a group of viral genes or between the genes of viral hosts (animals, plants, etc.), but they do not generally offer a study of the homology between them. The rare databases which compare viral and non-viral genetic sequences do not present phylogenetic trees. It was thus impossible up until recently to analyse on a large scale the exchanges of genes between cellular organisms and viruses. It is there that PhEVER has innovated. Containing the sequences of the ensemble of viral genomes, prokaryotes and eukaryotes, it is the first public database to allow the comparison between viral and non-viral sequences which come from entirely decoded and annotated genomes, thus supplying information which is useful for a study of the transfer of genetic material between the virus and the infected cell, as well as their evolution over the course of time.
PhEVER is thus a complete and unique database. It was moreover the subject of an article (1) published in January 2011 in Nucleic Acids Research, in which it can be observed that it is the fruit of work which is clearly multidisciplinary. In effect, whilst specialists in bioinformatics (a field which looks to answer biological questions whilst leaning on methods with origins in statistics, mathematics and computer science), the researchers behind this project were initially trained in a variety of domains: virologists and immunologists, mathematicians, physicists, etc. Amongst them is Leonor Palmeira, a biologist by training, who not long ago joined the University of Liège, within the Faculty of Veterinary Medicine’s Department of Infectious and Parasitical Diseases. Engaged in a wider project (Interaubio) set up at Lyon and aiming to study host-virus interactions through the development of numerous bioinformatics tools, it was her who was given responsibility for creating the PhEVER database. What were the steps taken?
(1) L. Palmeira, S. Penel, V. Lotteau, C. Rabourdin-Combe and C. Gautier. PhEVER: a database for the global exploration of virus–host evolutionary relationships Nucleic Acids Research, 2010, 1–7