pdm_utils

pdm_utils manages MySQL databases for phage genomics data, enabling storage, update, and retrieval of sequenced and annotated bacteriophage genomes to support comparative genomic analyses such as those produced by the SEA-PHAGES program.

Key Features:

• Database creation and maintenance: Utilities to initialize and update MySQL databases tailored for phage genomics datasets, including sequenced and annotated bacteriophage genomes.
• Data management: Systematic organization and programmatic updating of genomic sequences, gene annotations, and associated metadata within MySQL.
• Support for comparative genomics: Efficient storage and retrieval functions that facilitate comparative analyses of genetic diversity, evolutionary relationships, and functional genomics among phages.
• Customization for phage research: Phage-specific schema and tools configured to accommodate outputs typical of the SEA-PHAGES program and large-scale bacteriophage sequencing projects.

Scientific Applications:

• Genomic data storage: Centralized MySQL storage of phage genomic sequences and annotations for downstream analysis.
• Data exploration and analysis: Enabling query-driven extraction of sequences, annotations, and metadata to support pattern discovery and dataset curation.
• Comparative genomics: Supporting comparative studies to identify evolutionary relationships and functional variation among bacteriophage genomes.

Methodology:

Implemented in Python and integrated with MySQL; provides utilities for initializing and updating phage genomics databases with sequenced and annotated genomes.