phiSITE

Database of Gene Regulation in Bacteriophages

• Tools
  • Cluster-Buster - program for finding clusters of pre-specified motifs in nucleotide sequences
  • MCAST - discover motifs (highly conserved regions) in groups of related DNA or protein sequences
  • Promscan - scans DNA sequence for patterns
  • AlignACE - aligns Nucleic Acid Conserved Elements
  • FootPrinter - a program designed for phylogenetic footprinting

• Tool Packages
  • RSAT - provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences

• Databases
  • TRANSFAC - contains data on transcription factors, their experimentelly-proven binding sites, and regulated genes
  • PRODORIC - PROcariotIC Database Of Gene-Regulation
  • RegulonDB - Escherichia coli K12 transcriptional network
  • CoryneRegNet - Database of Corynebacterial Transcription Factors and Regulatory Networks
  • ViralZone - a knowledge resource to understand virus diversity
  • ICTVdB - The Universal Virus Database of the International Committee on Taxonomy of Viruses

• Other Tools
  • WEBLOGO - web based application designed to make the generation of sequence logos

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