title: Phagonaute: A web-based interface for phage synteny browsing and protein function prediction.
abstract: Distant homology search tools are of great help to predict viral protein functions. However, due to the lack of profile databases dedicated to viruses, they can lack sensitivity. We constructed HMM profiles for more than 80,000 proteins from both phages and archaeal viruses, and performed all pairwise comparisons with HHsearch program. The whole resulting database can be explored through a user-friendly "Phagonaute" interface to help predict functions. Results are displayed together with their genetic context, to strengthen inferences based on remote homology. Beyond function prediction, this tool permits detections of co-occurrences, often indicative of proteins completing a task together, and observation of conserved patterns across large evolutionary distances. As a test, Herpes simplex virus I was added to Phagonaute, and 25% of its proteome matched to bacterial or archaeal viral protein counterparts. Phagonaute should therefore help virologists in their quest for protein functions and evolutionary relationships.
authors.affiliation: Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Hadrien
authors.initials: H
authors.lastname: Delattre
authors.affiliation: Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Oussema
authors.initials: O
authors.lastname: Souiai
authors.affiliation: Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Khema
authors.initials: K
authors.lastname: Fagoonee
authors.affiliation: I2BC, CEA, Université Paris-Saclay, 91198 Gif-sur-Yvette, France. Electronic address: marie-agnes.petit@jouy.inra.fr.
authors.forename: Raphaël
authors.initials: R
authors.lastname: Guerois
authors.affiliation: Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France. Electronic address: raphael.guerois@cea.fr.
authors.forename: Marie-Agnès
authors.initials: MA
authors.lastname: Petit
mesh_terms: D001435:Bacteriophages / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D012984:Software; D026801:Synteny; D014764:Viral Proteins / Q000235:genetics* / Q000378:metabolism; D064878:Web Browser
chemical_list: D014764:Viral Proteins
keywords: Archaeal viruses; Bacteriophages; HSV1; Recombination functions