Transcription factors database 
Catch®  composite element search
cis-analyst  search for conserved clusters of transcription-factor binding sites.
CORG a database for comparative Regulatory Genomics.
DBTBS Bacillus trans factors
DBTSS Database of Transription Start Sites
DPinteract (E.coli) DPinteract (E.coli)
GenAtlas  fetch 10 Kb of upstream sequence for promoter analysis
GeneTide a new transcriptome focused  databases
Genomatix Software explore gene regulation network
JASPAR Transcription factor binding profile database.
Match™ matrix based search for transcription factor binding sites
ooTFD object oriented TF db
oPPOSUM retrieves matched mouse and human sequences  
PathoDB® Professional Pathologically altered transcription factors
PRESTA tool for transcription start point verification 
PRODORIC  prokaryotic database of gene regulation.
RegulonDB Transcriptional Regulation and Genome Organization
RSAT Regulatory Sequence Analysis Tools
Signal Scan Service Signal Scan Service
SiteSeer (Transfac 6.0) SiteSeer (Transfac 6.0)
Softberry DNA Sequence Analysis Tools
Stubb Allows users to look for clusters of binding sites 
Target Explorer  Creates customized libraries binding site matrices,
TESS  Transcription Factor Site Scan
TFSearch  uses Transfac 3.3
TFSS Transcription Factor Site Scan
TRANSCompel® Professional Composite elements database 
TRANSFAC The Transcription Factor Database
TRANSFAC® Professional  cis-acting regulatory DNA elements and trans-acting factors
TRED Transcriptional Regulatory Element Database
TRPD Transcription Regulatory Regions Database
YeaSTRACT Transcriptional Regulators And Consensus Tracking