- Promoter and Transcription Factors Databases
- Phylogenetic Footprinting
- Promoters in Groups of Genes
- Promoter Search Tools
- Transcription Binding Tools
- Transcription Start Site Prediction
- Transcription Terminator
- Prokaryote Promoters
Promoter and Transcription Factors Databases
- open in new windowAGRIS The Arabidopsis Gene Regulatory Information Server
- open in new windowPlantTFDB The Plant Transcription Factor Database
- open in new windowDATF Arabidopsis thaliana transcription factor database
- open in new windowEPD - Eukaryotic Promoter Database at EMBL, Heidelberg
- open in new windowdbTSS - database of Transcriptions Start Sites
- open in new windowJaspar - The high-quality transcription factor binding profile database
- open in new windowPlantCare - a Plant Promoters database
- open in new windowPlantPromDB - a Database of Plant Promoter Sequences
- open in new windowSCPD - the Promoter Database of Saccharomyces cerevisiae
- TFD - the IFTI-MIRAGE website
- open in new windowTransFac - Gene Regulation at BioBase
- open in new windowTRED - Transcriptional Regulatory Element Database
- open in new windowTRRD - Transcription Regulatory Regions Database
- open in new windowcisRED database holds conserved sequence motifs identified by genome scale motif discovery
- open in new windowRel/NF-kappaB target genesi
Phylogenetic Footprinting
- open in new windowConfac - Conserved Transcription Factor Binding Site Finder
- open in new windowConreal - CONserved Regulatory Elements anchored ALignment
- open in new windowConsite - Explore transcription factor binding sites shared by two genomic sequences
- open in new windowPROMH - Search for promoters/functional motifs
- open in new windowrVista - v2.0
Promoters in Groups of Genes
- open in new windowAlignACE - a program which finds sequence elements conserved in a set of DNA sequences from Church lab
Download program open in new windowHere - open in new windowCREME - Cis-REgulatory Module Explorer 2.0
- open in new windowGibbs motif sampler
- open in new windowMEME - The MEME/MAST System
- open in new windowMotifSampler - finds motifs in groups of sequences, and provides background models for cleaner predictions.
- open in new windowOTFBS - Over-represented Transcription Factor Binding Site Prediction Tool
- open in new windowPRIMA - a software for promoter analysis from Shamir's lab
- open in new windowPROMO - ALGGEN's Home Page (under research)
- open in new windowRSAT - Regulatory Sequence Analysis Toolsi
- open in new windowTrafac - UC/CHMC TraFaC Homology Server
- open in new windowVista - Tools for Comparative Genomics
- open in new windowToucan a workbench for regulatory sequence analysis on metazoan genomes
- open in new windowDiRE Distant Regulatory Elements
- open in new windowAthamap - a genome-wide map of potential transcription factor and small RNA binding sites in Arabidopsis thaliana
- open in new window MotifMogul a web server that enables the analysis of multiple DNA sequences using sets of Position Weight Matrices
- open in new windowImprobizer searches for motifs in DNA or RNA sequences that occur with improbable frequency
- open in new windowMotifViz Motif Search and Visualization
- open in new window GSEA - Gene Set Enrichment Analysis from BROAD institute
- open in new windowCarrie Computational Ascertainment of Regulatory Relationships (Inferred from Expression)
- open in new windowWebMotif from Fraenkel's lab
- open in new windowTFME - a software suite for identifying and analyzing transcription factor bindings sites
Promoter Search Tools
- open in new windowCorePromoter - Human Core-Promoter Prediction Program
- open in new windowNNPP Neural Network Promoter Prediction at Berkeley
- open in new windowPromoter2.0 - Prediction server at CBS
- open in new window PromoterInspector - Prediction of promoter regions in mammalian genomic sequences
- open in new windowPromoterScan - predicts putative eukaryotic Pol II promoter sequences
- open in new windowRegulatory Sequence Analysis Tools
- open in new windowSignalScan - Find and list homologies of published signal sequences with the input DNA sequence
- open in new windowSoftBerry tools - for gene regulation and promoter search
- open in new windowZhang Lab Tools - Promoter tools and databases for Human, Drosophila, C. Elegans, Arabidopsis, Yeast
- open in new windowZlab - many tools for gene regulation
Transcription Binding Tools
- open in new windowALIBABA predicts transcription factor binding sites by constructing matrices on the fly from TRANSFAC
- open in new windowCister - Cis-element Cluster Finder
- open in new windowCOMPEL - database on composite regulatory elements affecting gene transcription in eukaryotes
- open in new window RSA-tools - Regulatory Sequence Analysis tools - Search a pattern (string description) within all upstream or downstream regions of a genome
- open in new windowTESS - Predicting Transcription factors binding sites at CBIL, USA
- open in new windowTFSEARCH - searching Transcription Factor Binding Sites
- open in new windowTfsitescan - at IFTI
- open in new windowTRANSFAC - a database on eukaryotic cis-acting regulatory DNA elements and trans-acting factors
Transcription Start Site Prediction
- open in new windowDBTSS - Database of Transcriptional Start Sites
- open in new windowFirstEF - first-exon and promoter prediction program for human DNA
- open in new windowPromoSer - Human, Mouse and Rat promoter extraction service
- open in new windowTransFind Predicting transcriptional regulators for gene sets
Transcriptuion Terminator
- open in new windowTransTermHP finds rho-independent transcription terminators in bacterial genomes
Prokaryote Promoters
- open in new windowDbtbs Transcription Factors Regulated Operons
- open in new windowMicrobesOnline
- open in new windowProdoric a comprehensive database about gene regulation and gene expression in prokaryotes
- open in new windowPromscan
- open in new windowSoftberry
- open in new windowRibex
- open in new windowRegulonDB
- open in new windowTractorDB
- open in new windowRSAT