The SEED genome comparison environment

The SEED genome comparison environment performs automated annotation and comparative analysis of prokaryotic genomes to identify protein-encoding genes, rRNA and tRNA genes, assign gene functions, and reconstruct metabolic subsystems for studies in microbial ecology, evolution, and metabolism.

Key Features:

• Automated annotation: Identifies protein-encoding genes, rRNA genes, and tRNA genes in prokaryotic genome sequences.
• Functional assignment: Assigns functions to predicted genes to characterize gene roles within the organism.
• Subsystem prediction: Predicts metabolic subsystems and reconstructs metabolic networks represented in a genome.
• Comparative analysis environment: Enables exploration and comparison of annotated genomes against other annotated genomes maintained in The SEED database.
• Rapid turnaround: Delivers annotated genomes within a typical timeframe of 12-24 hours after submission.

Scientific Applications:

• Microbial ecology: Provides genome annotations and subsystem reconstructions to infer metabolic capabilities and ecological roles of microbes.
• Evolutionary biology: Supports comparative analyses to identify evolutionary relationships and trace genetic changes related to adaptation and speciation.
• Metabolism research: Enables reconstruction of organismal metabolic networks for studies of biochemical pathways and metabolic potential.

Methodology:

A fully automated pipeline integrates gene identification (protein-encoding genes, rRNA, tRNA), functional annotation, and metabolic network/subsystem reconstruction.