PaVE

PaVE provides a curated bioinformatic resource and database for papillomavirus genomes with integrated visualization and analysis tools.

Key Features:

• BLAST: Performs sequence similarity searches against the papillomavirus database.
• L1 typing tool: Classifies papillomavirus sequences based on the L1 gene region.
• Genome locus viewer: Visualizes genomic features and annotations of papillomavirus genomes.
• Phylogenetic tree generator: Generates phylogenetic trees for evolutionary analysis of papillomaviruses.
• Multiple sequence alignment: Aligns sequences using MAFFT.
• Protein structure viewer: Displays protein structures using Mol*, the embeddable viewer used by RCSB (Research Collaboratory for Structural Bioinformatics).
• Swagger API: Performs database queries and executes jobs for BLAST, MAFFT, and the L1 typing tool.

Scientific Applications:

• Papillomavirus genome analysis: Supports researchers and clinicians in studying papillomavirus genomes and their molecular biology.
• Viral classification and typing: Enables classification of papillomavirus types based on L1 gene sequence analysis.
• Phylogenetic analysis: Facilitates evolutionary studies of papillomavirus relationships through tree generation.
• Protein structure analysis: Allows examination of papillomavirus protein structures using integrated structure visualization.
• Sequence alignment: Supports comparative genomic analysis through multiple sequence alignment of papillomavirus sequences.

Methodology:

PaVE 2.0 uses a Python Flask framework with a JavaScript/JINJA template front end, a Neo4j database, and a Celery queue for longer running tasks. Multiple sequence alignment uses MAFFT. The protein structure viewer uses Mol*. A Swagger API performs database queries and executes jobs.