Automated Curation and Annotation of Viral Proteins

NCBI protein annotations (RefVirus) were first automatically curated (no upper case except in gene names, correction of typos, etc.). Phages for which all protein annotations was only an uninformative list (‘hypothetical protein GP1’, ‘hypothetical protein GP2’, etc.) were considered as unannotated. These protein annotations were first combined to determine an annotation for PHROGs. To refine this annotation, the 38 880 PHROGs were compared to different databases. PHROG profiles were compared to Pfam domains (version of jan 2018; 19 (link)) and UNICLUST (20 (link)) and individual viral protein were compared to proteins in KEGG Orthologous groups (KOs; version of jan 2018) using MMseq (bit-score>50, coverage >50%). Manual curation of the collected annotations and similarities allowed to extract a single annotation per PHROG.

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Terzian P., Olo Ndela E., Galiez C., Lossouarn J., Pérez Bucio R.E., Mom R., Toussaint A., Petit M.A, & Enault F. (2021). PHROG: families of prokaryotic virus proteins clustered using remote homology. NAR Genomics and Bioinformatics, 3(3), lqab067.

Publication 2021

Gene Phages Protein annotations Proteins Viral protein

Corresponding Organization : Microbiologie de l’alimentation au service de la santé

Other organizations : Laboratoire de Microbiologie et Génétique Moléculaires, Laboratoire Jean Kuntzmann, Université Grenoble Alpes, Institut polytechnique de Grenoble, Universidad Nacional Autónoma de México, Université Libre de Bruxelles

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Protocol cited in 40 other protocols

Variable analysis

independent variables

NCBI protein annotations (RefVirus) were first automatically curated (no upper case except in gene names, correction of typos, etc.)
Phages for which all protein annotations was only an uninformative list ('hypothetical protein GP1', 'hypothetical protein GP2', etc.) were considered as unannotated
These protein annotations were first combined to determine an annotation for PHROGs
PHROG profiles were compared to Pfam domains (version of jan 2018; 19 (link)) and UNICLUST (20 (link))
Individual viral protein were compared to proteins in KEGG Orthologous groups (KOs; version of jan 2018) using MMseq (bit-score>50, coverage >50%)

dependent variables

Annotation for PHROGs

control variables

Manual curation of the collected annotations and similarities

Annotations

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