phiSITE

phiSITE catalogs over 700 experimentally confirmed or predicted regulatory elements (promoters, operators, terminators, and attachment sites) across 32 bacteriophages from the Siphoviridae, Myoviridae, and Podoviridae families to support studies of phage gene regulation.

Key Features:

• Regulatory element dataset: Contains over 700 experimentally confirmed or predicted promoters, operators, terminators, and attachment sites across 32 bacteriophages.
• Manual curation and cross-references: Data curated from scientific literature and cross-referenced with EMBL, UniProt, NCBI taxonomy, NCBI Genome, ICTVdb, and PubMed Central.
• SQL-based data management: Uses an SQL-based system to manage the dataset.
• Full-text search: Enables retrieval of specific regulatory elements via full-text queries.
• Graphical genome visualizations: Provides phage genome visualizations for structural and regulatory analysis.
• Export options: Supports export in multiple formats for integration with external bioinformatics tools.
• Gene regulatory network visualizations: Provides detailed gene regulatory network visualizations for Bacillus phage GA-1, Enterobacteria phage lambda, Enterobacteria phage Mu, Enterobacteria phage P2, and Mycoplasma phage P1.

Scientific Applications:

• Study of phage gene regulation: Enables analysis of regulatory elements and their roles in bacteriophage gene expression.
• Gene regulatory network analysis: Supports analysis of gene regulatory networks for the five phages with network visualizations.
• Support for molecular genetics and bioinformatics: Provides curated regulatory data and analysis outputs for molecular genetics and bioinformatics research.

Methodology:

SQL-based data management, manual literature curation with cross-references to EMBL/UniProt/NCBI taxonomy/NCBI Genome/ICTVdb/PubMed Central, full-text search, graphical genome visualizations, export in multiple formats, and gene regulatory network visualization for specified phages.