MarDB

MarDB provides access to an extensive collection of incomplete marine prokaryotic genomes and associated metadata to support marine microbial, metagenomic, and environmental genomics research.

Key Features:

• Inclusion Criteria: MarDB encompasses sequenced marine prokaryotic genomes irrespective of completion, representing various stages of sequencing completeness.
• Rich Metadata Annotation: Each record is annotated with 106 metadata fields covering sampling methods, sequencing techniques, assembly processes, annotation details, organism-specific information, and taxonomic classification.
• Integration with Ontologies: MarDB employs ontologies and controlled vocabularies within its contextual databases to maintain metadata consistency and interoperability.
• BLAST Search Support: The database supports BLAST searches against corresponding sequence databases for comparative genomic and functional analyses.
• Integration with Marine Metagenomics Portal (MMP): MarDB is integrated within the Marine Metagenomics Portal, linking contextual metadata with sequence repositories.

Scientific Applications:

• Marine Microbiology: Supports analyses of marine microbial communities and organismal genomics.
• Metagenomics and Environmental Genomics: Enables interpretation of metagenomic assemblies and environmental sequencing datasets using incomplete genomes and metadata.
• Microbial Diversity and Evolutionary Biology: Facilitates studies of microbial diversity and evolutionary relationships among marine prokaryotes.
• Ecological Function Inference: Aids investigation of ecological functions and potential roles of microorganisms within marine ecosystems.
• Study of Uncultivable Microorganisms: Provides genomic access to uncultivable or poorly characterized marine microorganisms for genetic and functional insights.

Methodology:

Integration of richly annotated contextual databases with sequence data repositories; use of controlled vocabularies and ontologies to ensure metadata consistency.