Introduction
Binding site discovery:
-Computational -Experimental
Cis-regulatory evolution
Organisms
-Yeast
-Fly
-Mouse
-Human
Binding site degeneracy
Functional variants
Cis-regulatory code
Regulatory networks

Fly

Databases and datasets
REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs)
DBSD: - Drosophila binding site database

Software and tools
eCIS-ANALYST searches the Drosophila melanogaster and Drosophila pseudoobscura genomes for conserved clusters of transcription-factor binding sites.
Stubb - Allows users to look for clusters of transcription factor binding sites in one or two aligned species and, for fly data, view the results superimposed on the D.melanogaster annotations via Gbrowse.
Target Explorer - Allows users to create customized libraries of transcription factor binding site matrices, search for clusters and combinations of binding sites, retrieve FlyBase annotation for nearby genes, and generate graphical representations of binding sites.