External Resources

Promoter Databases

EPD - Eukaryotic Promoter Database
DBTSS - DataBase of Transcriptional Start Sites (human)
SCPD - Saccharomyces cerevisiae promoter database
DCPD - Drosophila core promoter database
PlantProm DB - Plant Promoter Sequences
CSHLmpd - Mammalian Promoter Database
PromEC - E. coli promoters

Promoter Prediction

DoOP - Database of Orthologous Promoters
First Exon Finder, CorePromoter and CpGpromoter
CpGProD - CpG island promoter detection
McPromoter
PromoterInspector
Promoter 2.0
PromFD
NNPP

Gene Expression Databases

Gene Expression Omnibus
ArrayExpress
Stanford Microarray Database
ExpressDB
SAGE Genie

Microarray Analysis Software

VERA and SAM
Wong Lab software
SAM: Significance Analysis of Microarrays
GSEA
Eisen Lab software
Bioconductor

Phylogenetic Footprinting
TraFaC

PipMaker
VISTA
LAGAN Toolkit
SeqComp and FamilyRelations
Bayesian Phylogenetic Footprint
ConSite
FootPrinter

CpG Islands

CpG Island Searcher

Repeat Detection

RepeatMasker
nseg
dust
Tandem Repeats Finder

Sequence and Annotation Visualization

Alfresco
Artemis
Ensembl
UCSC Genome Browser
NCBI Map Viewer

Transcription Factor, Binding Site & Motif Databases & Analysis Tools

JASPAR
TRANSFAC - public
GeneExpress / TRRD
RegulonDB
DBTBS - A Database of Bacillus Subtilis Promoters and Transcription Factors
PRODORIC - A Database of prokaryotic gene regulation

Motif Search

Patser
MATCH - public
BindGene
TFbind
MatInspector and ConsInspector
TESS
TFSEARCH
PROMO
MDscan - uses ChIP-on-chip data

Motif Cluster Search

MSCAN
Cis-analyst
Fly enhancer

Ab-initio Motif Discovery

Gibbs Motif Sampler
AlignACE
BioProspector
Motif Sampler
SeSiMCMC
Consensus and Co-Bind
ANN-Spec
MEME
YMF
MultiProfiler
cis-Site Seeker
CoreSearch
MACAW - Multiple Alignment Construction & Analysis Workbench
Melina

Motif Overrepresentation

PRIMA

Pipelined Analysis Programs

Regulatory Sequence Analysis Tools
Toucan
INCLUSive