SUMMARY: Bacteriophages (phages) are incredibly abundant and genetically diverse. The volume of phage genomics data is rapidly increasing, driven in part by the SEA-PHAGES program, which isolates, sequences and manually annotates hundreds of phage genomes each year. With an ever-expanding genomics dataset, there are many opportunities for generating new biological insights through comparative genomic and bioinformatic analyses. As a result, there is a growing need to be able to store, update, explore and analyze phage genomics data. The package pdm_utils provides a collection of tools for MySQL phage database management designed to meet specific needs in the SEA-PHAGES program and phage genomics generally. AVAILABILITY AND IMPLEMENTATION: https://pypi.org/project/pdm-utils/.

The Actinobacteriophage Database (PhagesDB) is a comprehensive, interactive, database-backed website that collects and shares information related to the discovery, characterization and genomics of viruses that infect Actinobacterial hosts. To date, more than 8000 bacteriophages-including over 1600 with sequenced genomes-have been entered into the database. PhagesDB plays a crucial role in organizing the discoveries of phage biologists around the world-including students in the SEA-PHAGES program-and has been cited in over 50 peer-reviewed articles. Availability and Implementation: http://phagesdb.org/. Contact: [email protected].

BACKGROUND: Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation. RESULTS: We describe here a bioinformatic tool, Phamerator, that assorts protein-coding genes into phamilies of related sequences using pairwise comparisons to generate a database of gene relationships. This database is used to generate genome maps of multiple phages that incorporate nucleotide and amino acid sequence relationships, as well as genes containing conserved domains. Phamerator also generates phamily circle representations of gene phamilies, facilitating analysis of the different evolutionary histories of individual genes that migrate through phage populations by horizontal genetic exchange. CONCLUSIONS: Phamerator represents a useful tool for comparative genomic analysis and comparative representations of bacteriophage genomes.