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Local Resources (Zlab)

Promoser - human, mouse and rat promoter extraction service
Possum - simple matrix-based motif search
CARRIE - Generate transcriptional regulatory networks from microarray and promoter sequence data.
CisML - An XML format for Sequence Motif Detection Programs.
HuGE Index - database of gene expression in normal human tissues
Cis-element information - count matrices and background info for some cis-elements
site2genome - locate sites in the human, mouse and rat genomes
REPFIND - find clustered, exact repeats in nucleotide sequences
ICSF - identifies conserved structural features at sequentially degenerate locations in transcription factor binding sites

Tools to find motif clusters in DNA sequences

Cluster-Buster (newest method - our favorite!)
Comet (includes statistical significance estimates)
Cister (our original method)

Tools to find diagnostic motifs in a set of regulatory (e.g. promoter) sequences

GLAM - gapless local alignment of multiple sequences (motif discovery)
Clover - find overrepresented motifs in DNA sequences
ROVER - find relatively overrepresented motifs in DNA sequences. New Java Version Available
MotifViz - Integration of tools for detecting overrepresented motifs
SeqVISTA - a viewer of sequences and their annotations; now with a Motif module for integrating transcriptional regulation analysis tools.