MicrobeAnnotator

MicrobeAnnotator annotates microbial genomes from Bacteria, Archaea, and Viruses, producing protein-level annotations and KEGG-module-based metabolic reconstructions to enable comparative high-throughput analysis.

Key Features:

• Automated Workflow: A fully automated pipeline that integrates multiple reference protein databases to perform genome annotation without manual step orchestration.
• Iterative Annotation Approach: Employs an iterative strategy starting from proteins predicted by user-selected ORF prediction tools, such as Prodigal, with pipeline configurations composed of three or five main steps depending on the selected "flavor".
• Integration with Multiple Databases: Combines results from several reference protein databases to enhance annotation confidence and coverage.
• Metabolic Reconstruction Summaries: Produces summaries of metabolic reconstructions leveraging KEGG modules for high-throughput analysis and comparison of metabolic potential.
• Input Scope: Supports genomes derived from isolates, single cells, and metagenomes.

Scientific Applications:

• Isolate and single-cell genome annotation: Generates protein annotations and metabolic reconstructions for individual microbial genomes from isolates and single-cell assemblies.
• Metagenome-derived metabolic profiling: Enables annotation and metabolic inference from metagenome-assembled genomes to assess community metabolic potential.
• Comparative analyses in ecology, evolution, and biotechnology: Facilitates comparison of metabolic capabilities across genomes for studies in microbial ecology, evolution, and biotechnology applications.

Methodology:

Protein prediction using user-selected ORF tools (e.g., Prodigal); iterative refinement of annotations by cross-referencing multiple reference protein databases; metabolic reconstructions derived from KEGG modules; pipeline variants implemented as three- or five-step workflows.