PHASTEST

PHASTEST identifies and annotates prophage sequences and other gene types (protein-coding regions, tRNA, tmRNA, and rRNA) in bacterial genomes and plasmids to support rapid prophage detection and whole-genome annotation.

Key Features:

• Enhanced speed and accuracy: PHASTEST reports ~31% faster runtime than PHASTER and a 2–3% increase in prophage identification accuracy, processing a typical bacterial genome in approximately 3.2 minutes from raw sequence data or ~1.3 minutes from pre-annotated GenBank files.
• Comprehensive genome annotation: Provides whole-genome annotations including protein-coding regions, tRNA, tmRNA, rRNA sequences, and annotated prophage regions.
• Genome visualization: Produces annotated genome maps for visualization of prophages and other genomic features.
• Programmatic access and deployment: Supports an API for programmatic queries and a Docker image for local installation.
• Multiple-query and comparative analysis: Supports multiple (metagenomic) queries and automated look-ups against thousands of previously annotated bacterial genomes.
• Lineage: Successor to PHAST and PHASTER with extended annotation capabilities.

Scientific Applications:

• Prophage identification and annotation: Detection and annotation of prophage sequences in bacterial genomes and plasmids.
• Whole-genome annotation: Annotation of protein-coding genes, tRNA, tmRNA, and rRNA across bacterial genomes.
• Metagenomic analysis: Analysis of multiple queries from metagenomic datasets to identify prophages and genomic features.
• Comparative genomics: Automated look-ups against thousands of annotated bacterial genomes to support comparative studies.

Methodology:

Processes raw sequence data or pre-annotated GenBank files to perform prophage identification and whole-genome annotation, and performs automated look-ups against thousands of previously annotated bacterial genomes while providing programmatic access via an API and distribution via a Docker image.