Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages

Background:
Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are still at the surface level. Among phages, some adopt the lysogenic mode of infection, where the genome integrates into the host cell genome, forming a prophage. Prophages enable viral genome replication without host cell lysis and often contribute novel and beneficial traits to the host genome. Despite their importance, research on prophages is limited. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.
Results:
To bridge this gap, the creation of Prophage-DB, a prophage database, aims to a..., , , # Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages

[https://doi.org/10.5061/dryad.3n5tb2rs5](https://doi.org/10.5061/dryad.3n5tb2rs5)

This dataset contains prophage sequences (available as .fna files) identified from prokaryotic genomes from three public databases (Genome Taxonomy Database (GTDB) (release 207), National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (accessed March 2023), and Searchable Planetary-scale mIcrobiome REsource (SPIRE). The downloaded prokaryotic genomes from these databases contained both archaeal and bacterial representative genomes (SPIRE also included data from unknown hosts). 

## Methods

Prophage identification from downloaded representative genomes was carried out using VIBRANT (v1.2.1). We used the default arguments when using VIBRANT (minimum scaffold length requirement = 1000 base pairs, minimum number of open readings frames (ORFs, or proteins) per scaffold requi...