Beav

Beav automates the annotation of bacterial genome sequences, mobile genetic elements, molecular systems and gene clusters, key regulatory features, and other elements to enable comprehensive and accurate genome annotation for inferring predicted organism functions.

Key Features:

• Mobile Genetic Element Annotation: Beav annotates integrative and conjugative elements, phages, and other mobile genetic elements that are often not annotated by existing pipelines.
• Gene Cluster and Molecular System Annotation: Beav annotates loci encoding secretion systems, biosynthetic gene clusters, and other larger elements that provide important genomic context.
• Regulatory Feature Annotation: Beav annotates key regulatory features as part of its comprehensive genome annotation.
• Custom Databases for Plant-Associated Microbes: Beav incorporates custom databases to improve annotation of key virulence and symbiosis genes in agriculturally important pathogens and mutualists.
• Agrobacterium-Specific Pipeline: Beav includes an optional pipeline that identifies and classifies oncogenic plasmids and annotates plasmid-specific features.
• Consolidated Output: Beav consolidates all annotations to produce a single comprehensive output following the completion of all analyses.
• Genome and Plasmid Map Generation: Beav generates publication-quality genome and plasmid maps.

Scientific Applications:

• Comprehensive Bacterial Genome Annotation: Beav enables annotation of diverse genome features including genes, mobile genetic elements, molecular systems, and gene clusters for understanding functions encoded by an organism.
• Plant-Associated Microbe Research: Beav improves annotation of virulence and mutualism loci in plant-associated bacteria that are often misannotated by existing pipelines.
• Horizontal Gene Transfer Analysis: Beav annotates mobile genetic elements that can horizontally mobilize genes encoding virulence, antimicrobial resistance, or other adaptive functions.
• Agrobacterium Genomics: Beav provides specialized identification and classification of oncogenic plasmids and plasmid-specific feature annotation for Agrobacterium species.

Methodology:

Beav uses existing tools in addition to custom models, scripts, and databases to annotate diverse elements, systems, and sequence features.