TOOLS:

1. Search for regions of homology

Blast search TRRD database

BinomSite2 program 
You may perform the search for regions homologous to the transcription factor binding sites described in TRRD in the sequence of interest. The program BinomSite performs the search by binomial probability estimation of the similarity between fragments of user’s sequence and each of the transcription factor binding sites described in TRRD.

2. Tools for analysis of DNA sequences

SITECON
A program package for detection and analysis of conservative conformational and physicochemical properties in sets of transcription factor binding sites. It contains the knowledge base of conservative properties of transcription factor binding sites. This resource contains also a tool for recognition of potential binding sites based on the data about conservative properties of the site in a user-specified genomic sequence

SiteGA
For transcription factor binding  site recognition using genetic algorithm

ARGO
A web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters