Genome information

• NCBI complete genomes. Bacterial + a few other genomes installed in RSAT are parsed from the NCBI complete genome repository.
• Ensembl. Main data source for metazoan genomes installed in RSAT.

Regulatory sequence analysis

Databases on transcriptional regulation

• PAZAR - One stop shopping experience for transcription factors and regulatory sequence annotations. It is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). Our goal is to be the public repository for regulatory data.
• ORegAnno - An open access database for gene regulatory element and polymorphism annotation
• SCPD - A promoter database of the yeast Saccharomyces cerevisiae
• TRED - Transcriptional Regulatory Element Database
• YeaSTRACT - Yeast Search for Transcriptional Regulators And Consensus Tracking.
• TRANSFAC - The Transcription Factor Database
• JASPAR - The high-quality transcription factor binding profile database.
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• OOTFD - object-oriented transcription factors database
• RegulonDB - A Database on Transcriptional Regulation and Genome Organization
  New interface to RegulonDB
• PRODORIC - prokaryotic database of gene regulation.
• DPinteract (E.coli)
• DBTBS - a database of Bacillus subtilis promoters and transcription factors
• CORG - a database for COmparative Regulatory Genomics.
• T-Reg Comparator This web application allows you to compare a set of position weight matrices (PWM) against the T-Reg database. T-Reg is a relational database on transcriptional regulation that contains a collection of PWMs.

Transcription start sites

• EPD - The Eukaryotic Promoter Database.
• PromoSer - Human, Mouse and Rat promoter extraction service .
• DBTSS Database of Transcription Start Sites.

Retrieval of regulatory sequences

• EnsEMBL - a software system which produces and maintains automatic annotation on selected eukaryotic genomes.
• Biomart: retrieval of genomic sequences from EnsEMBL - BioMart is a query-oriented data management system developed jointly by the European Bioinformatics Institute (EBI) and Cold Spring Harbor Laboratory (CSHL).

motif discovery

• BioProspector
• CompareProspector - Eukaryotic regulatory element conservation analysis and identification using comparative genomics
• MDscan
• Improbizer
• Ann-spec
• MITRA- MIsmatch TRee Algorithm for Motif Discovery: Version 1.0
• GLAM - Gapless Local Alignment of Multiple Sequences
• INCLUSive - A suite of web-based tools for the automatic multistep analysis of microarray data
  • Motif Sampler - A gibbs sampler with organism-specific higher order (Markov) models for estimating prior frequencies.
  • Toucan - A workbench for regulatory sequence analysis on metazoan genomes,
• YRSA - Yeast Regulatory Sequence Analysis
• YMF - Finds short motifs in DNA sequences
• Consensus server
• patser, consensus and other stand-alone applications developed by in Gary Stormo's lab.
• Sequence Motif Discovery at EBI
• MEME
• YEBIS
• Signal Search Analysis Server. SSA is a software package for the analysis of nucleic acid sequence motifs that are postionally correlated with a functional site such as a transcription initiation site for instance.

Comparing discovered motifs with libraries

• TomTom. Compare your DNA motif against a database of known motifs (e.g., JASPAR, TRANSFAC, FlyReg, ...).
• T-Reg Comparator - compare a set of position weight matrices (PWM) against the T-Reg database, a relational database on transcriptional regulation that contains a collection of PWMs.
• STAMP - Alignment, Similarity, & Database Matching for DNA Motifs

Pattern search with libraries

• Transfac-associated programs (Matinspector, PatternSearch, SaGa).
• Web Signal Scan Service
• Web Promoter Scan Service
• SCPD - search putative sites

Detection of cis-regulatory modules (enhancer regions, composite elements)

• Target Explorer

Promoter prediction

• Dragon genome explorer
• Promoter 2.0. Promoter2.0 predicts transcription start sites of vertebrate PolII promoters in DNA sequences
• McPromoter V3. The Markov Chain Promoter Prediction Server University of Erlangen-Nuremberg (Germany). A statistical tool for the prediction of transcription start sites in eukaryotic DNA
• Promoter scan II. Eukaryotic Pol II Promoter Prediction
• Neural Network Promoter Prediction. Eukaryotes and prokaryotes.

Phylogenetic footprinting

• CompareProspector
• Bayesian Phylogenetic Footprint Homepage
• FamilyJewels. These tools were designed for computing and visualizing comparative analyses of two homologous eukaryotic genomic regions, with a focus on finding conserved non-coding regions of DNA that may encode regulatory linkages.
• TRES - Transcription Regulatory Element Search a tool for Comparative Promoter Analysis.
• FootPrinter
• Orthoseq - alignment and exon prediction in orthologous nucleotide sequences.
• CREME: A Framework for Identifying Cis-Regulatory Modules in Human-Mouse Conseved Segments
• ConSite
• Tools for phylogenetic footprinting purposes
• PhyloCon - Phylogenetic Consensus for Regulatory Motif Identification

Predicted elements in whole genomes

• rVista - identification of evolutionary conserved transcription factor binding sites
• UCSC HMR conserved transcription factor binding sites

Seqence logos

• Weblogo - logo drawing from aligned sequences
• GENIO/logo - RNA/DNA & Amino Acid Sequence Logos

Other tools for regulatory sequence analysis

• AG Biodiv
  • Genome Inspector

Microarray Data Analysis

• yMGV - yeast Microarray Global Viewer
• Expression profiler - a set of tools for the analysis and clustering of gene expression and sequence data.
• Arabidopsis Functional Genomics Consortium (AFGC)
• Stanford Microarray Database
• CATMA - A Complete Arabidopsis Transcriptome Microarray

Genome centers

Yeast-specific databases

• YETI - Yeast Exploration Tool Integrator
• SGD - Saccharomyces Genome Database
• MIPS - Yeast Genome Project Page
• Yeast genomes at MIT
• Yeast genome comparison at Stanford
• Saccharomyces Genome Sequencing at the GSC - WUSTL
• YPD - Yeast Protein Database)
• SCPD - A promoter database of the yeast Saccharomyces cerevisiae
• YTPdb - The yeast transporter database
• yMGV - yeast Microarray Global Viewer

Plasmodium falciparum genome

• PlasmoDB - the Plasmodium genome database.

Arbidopsis genome

• The Arabidopsis Information Resource

Human genome analysis

• Genome Browser
• RIKEN

Tutorials and courses

• Comparative genomics and phylogenetic footprints (by Philippe Gautier).
  A practical course on the utilization of comparative genomics approaches to detect regulatory elements in mammalian promoters. Slides with notes + tutorial + on-line help for each step of the tutorial.