RAST

RAST annotates complete or nearly complete bacterial and archaeal genomes to assign gene functions, predict metabolic subsystems, and reconstruct metabolic networks.

Key Features:

• Automated annotation: Performs automated structural and functional annotation of complete or nearly complete prokaryotic genomes.
• Gene identification: Identifies protein-encoding genes as well as rRNA and tRNA genes.
• Functional assignment: Assigns functions to predicted genes using subsystem-based approaches.
• Metabolic subsystem prediction: Predicts which metabolic subsystems are present in the genome.
• Metabolic network reconstruction: Reconstructs corresponding metabolic networks from predicted subsystems and gene functions.
• Comparative genomics: Enables comparative genomic analyses against genomes stored in the SEED database.
• Quality metrics: Emphasizes annotation accuracy, consistency, and completeness.
• Annotation turnaround: Typically provides annotations within 12–24 hours of submission.

Scientific Applications:

• Genome annotation: Produce standardized annotations for bacterial and archaeal genomes.
• Functional profiling: Determine functional capabilities of prokaryotic genomes through gene function assignment and subsystem prediction.
• Metabolic reconstruction: Reconstruct metabolic networks for metabolic pathway and network analyses.
• Comparative genomics: Compare annotated genomes using the SEED database to identify shared and unique subsystems and functions.

Methodology:

Identifying protein-encoding genes as well as rRNA and tRNA genes; assigning functions to these genes; predicting which metabolic subsystems are present; and reconstructing the corresponding metabolic network.