Genome annotation is the process of identifying functional elements along the sequence of a genome. The Genome Annotation Service in BV-BRC uses the RAST tool kit (RASTtk) to annotate genomic features in bacteria, the Viral Genome ORF Reader (VIGOR4) to annotate viruses, and PHANOTATE to annotate bacteriophages. All public genomes in BV-BRC have been consistently annotated with these services. Researchers can also submit their own private genome to the annotation service, where it will be deposited into their private workspace for their perusal and comparison with other BV-BRC genomes using BV-BRC analysis tools and services, e.g., Phylogenetic Tree, Genome Alignment, Protein Family Sorter, Comparative Pathway Viewer, Similar Genome Finder.
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.
There are three distinct application service specifications defined here:
- GenomeAnnotation: Service that provides the backend for the BV-BRC web interface; it takes contigs as input.
- GenomeAnnotationGenbank: Currently only available via the
p3-submit-genome-annotationcommand-line script; allows the processing of Genbank files as input. - ComprehensiveGenomeAnalysis: Provides the backend for the BV-BRC Comprehensive Genome Annotation service.
The code in this module provides the BV-BRC application service wrapper scripts for the genome annotation service as well as some backend utilities:
| Script name | Purpose |
|---|---|
| App-ComprehensiveGenomeAnalysis.pl | App script for the comprehensive genome analysis service |
| App-GenomeAnnotation.pl | App script for the genome annotation service |
| App-GenomeAnnotationGenbank.pl | App script for the genome annotation service for use with genbank files |
| p3x-process-genbank-batch.pl | (Experimental) Script for bulk processing of genbank batches |
| p3x-reindex-genome.pl | (Experimental) Script to resubmit the Solr indexing data for a set of genomes |
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