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Updated: Mar 20, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Published on: June 11, 2015
Phagonaute: A web-based interface for phage synteny browsing and protein function prediction
Hadrien Delattre1, Oussema Souiai1, Khema Fagoonee1
1Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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.
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