Transcription factor binding site prediction tools/software/Web-server

General

• SeqMotifs - A Suite of Web-based Programs to Search for Regulatory Motifs in Prokaryotes and Eukaryotes
  
• Resource on Gene expression regulatory sites and transcription factors
  
• DBD - Taxonomically broad transcription factor predictions: new content and functionality

Prokaryotes

• BioProspector - Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes
  
• PRODORIC - Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes
  
• PRE Detector - Prokaryotic Regulatory Elements Detector
  
• PRODORIC DB - Prokaryotic database of gene regulation
  
• REGULON - Bioinformatics resources for the study of gene regulation in bacteria
  
• FGENESB - Bacterial Operon and Gene Prediction

Eukaryotes

• CompareProspector - Eukaryotic Regulatory Element Conservation Analysis and Identification using Comparative Genomics