Artemis

Artemis visualizes and annotates genomic sequence data to support analysis and interpretation of microbial genomes (bacteria and archaea) and lower eukaryotes.

Key Features:

• Integrated Visualization: Visualizes sequence features, next-generation sequencing data, and analysis results in the context of a reference genome, including six-frame translations.
• Annotation Capabilities: Enables manual gene prediction and addition of biological annotations, facilitating identification of genomic features such as pathogenicity islands.
• Data Compatibility: Reads and writes EMBL, GenBank, and GFF file formats.
• Database Integration: Supports relational database schemas including the GMOD Chado schema for complex annotations and management of large or fragmented genome assemblies.
• Additional Tools: Includes the Artemis Comparison Tool (ACT) for comparative genomics and the Gene Builder tool for editing gene models and functional annotations using standard ontologies and controlled vocabularies.

Scientific Applications:

• Genome re-sequencing and variation detection: Supports genome re-sequencing projects and population-scale variation detection analyses.
• Whole-transcriptome sequencing: Supports visualization and annotation of whole-transcriptome sequencing data.
• Genome-wide analysis of protein-bound nucleic acids: Supports analysis of protein-bound nucleic acids across genomes.
• Comparative genomics: Enables comparative genomic analysis between sequences and assemblies via ACT.
• Microbial and compact-genome annotation: Applied to annotation and feature identification in compact genomes such as bacteria, archaea, and lower eukaryotes.

Methodology:

Integrates computational analysis with visual representation and supports multiple sequence formats and the GMOD Chado relational schema for data management and shared annotations.