MAS

MAS facilitates manual functional annotation of prokaryotic and viral genomes by integrating homology search results, annotation management, and standardized export formats.

Key Features:

• Annotation Management: Edit annotations, track annotation history and progress, and store data in a relational database.
• Homology Search Integration: Support for BLASTp, RPS-BLAST, and HHsearch against Swiss-Prot, nr, CDD, PDB, and an internally generated database to identify coding regions and infer gene function.
• Collaborative and HPC Compatibility: Multi-user operation over a LAN and compatibility with high-performance computing schedulers SGE and SLURM.
• Data Export: Export annotations and sequence data in FASTA, GenBank, GFF, and Excel formats.
• Project Organization and Comparison: Structure the annotation workflow to generate, interpret, and compare results from multiple analytical tools.

Scientific Applications:

• Manual Functional Genome Annotation: High-quality manual curation of prokaryotic and viral genomes.
• Homology-Based Gene Function Identification: Identification of coding regions and determination of gene function via BLASTp, RPS-BLAST, and HHsearch against Swiss-Prot, nr, CDD, PDB, and internal databases.
• Collaborative Annotation Projects: Team-based annotation workflows leveraging LAN and HPC resources for shared projects.

Methodology:

Performs homology searches using BLASTp, RPS-BLAST, and HHsearch against Swiss-Prot, nr, CDD, PDB, and an internal database; stores annotation data in a relational database; supports execution on HPC via SGE or SLURM; exports results in FASTA, GenBank, GFF, and Excel formats.