GAMOLA2

GAMOLA2 annotates and curates microbial genomes, producing gene models and functional, structural, and contamination annotations for bacteria, archaea, and viruses.

Key Features:

• Gene Model Determination: Incorporates algorithms to predict gene models and identify coding sequences within microbial genomes.
• Functional Annotation Tools: Executes BLAST searches and assigns functions using databases including COG, Pfam, and TIGRfam.
• Structural Predictions: Detects tRNAs, rRNA genes, non-coding RNAs, signal peptide cleavage sites, transmembrane helices, CRISPR repeats, and vector sequence contaminations.
• Modular Design: Employs a modular architecture that allows integration of additional computational functionalities.
• Artemis Integration: Integrates with a customized Artemis Genome Viewer for genomic visualization and manual curation.
• Supplemental Modules: Supports creation of custom BLAST databases, annotation transfer between genome versions, and preparation of GenBank files for submission via NCBI Sequin.

Scientific Applications:

• Microbial genome annotation and curation: Produces comprehensive annotations for bacterial, archaeal, and viral genomes.
• Functional assignment and comparative analysis: Assigns gene functions using BLAST and reference databases (COG, Pfam, TIGRfam) to support functional analyses.
• Structural feature and contaminant detection: Identifies tRNAs, rRNAs, ncRNAs, signal peptides, transmembrane regions, CRISPR repeats, and vector contaminations for quality control.
• Submission preparation: Generates GenBank files formatted for submission via NCBI Sequin.
• Database and version management: Enables creation of custom BLAST databases and annotation transfer between genome versions.

Methodology:

Performs gene model prediction; runs BLAST searches and annotates against COG, Pfam, and TIGRfam; detects tRNAs, rRNA genes, and non-coding RNAs; predicts signal peptide cleavage sites and transmembrane helices; recognizes CRISPR repeats and vector sequence contaminations; supports creation of custom BLAST databases, annotation transfer, and GenBank file preparation for NCBI Sequin; operates primarily within a Linux environment and integrates with the Artemis Genome Viewer for visualization and manual curation.