Papillomavirus Bioinformatics Resource

National Institute Of Allergy And Infectious Diseases

Investigators

Linked publications, trials & patents

Abstract

The PapillomaVirus Episteme (PaVE) has been established to provide information and bioinformatics resources to the scientific community for research on the Papillomaviridae family of viruses. The PaVE consists of a relational database and web applications that support the storage, annotation, analysis, and exchange of information. PAVE can be found at http://pave.niaid.nih.gov PaVe contains genomic and protein sequences for all papillomaviruses. It includes a multiple sequence alignment tool, a protein structure viewer, a viral typing tool and an Image viewer for visualizing clinical manifestations of viral infection. Linked review articles provided detailed information about all aspects of functional genomics of papillomaviruses. In FY2022, the PaVE database and website was updated and currently contains 665 annotated papillomavirus genomes (including 224 Non-reference genomes), 7361 genes and regions, 5397 protein sequences, and 77 protein structures, which users can explore, analyze or download. In April 2022, we released PaVE 2.0. The underlying libraries and hosting platform of PaVE have been completely upgraded and rebuilt as the original >10-year-old software framework has been deprecated. The PaVE 2.0 team in the Bioinformatics and Computational Biosciences Branch has developed open-source GoCD pipelines for CI/CD (continuous integration and deployment) of both applications and data (now in S3 cloud storage). PaVE 2.0 is hosted on an on-demand virtual server using the NIAID Operations & Engineering Branchs Monarch tech stack and Amazon Web Services. The framework has been upgraded to Python Flask with a JavaScript/JINJA template front end and the database switched from MySQL to Neo4j. A Swagger API (application programming Interface) performs all database queries, and executes jobs for BLAST, MAFFT, and the L1 typing tool (all updated) ) and will allow potential future programmatic access to the data. A new Celery stack supports longer running tasks (such as large BLAST jobs and the L1 typing tool) and multiple sequence alignment will now use MAFFT instead of CLUSTAL. This resource is invaluable for the papillomavirus research community. PaVE has been cited 645 times on Google Scholar