Toolbox > Sequence Analysis > Promoters
  • 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

  • AGRIS The Arabidopsis Gene Regulatory Information Serve
  • PlantTFDB The Plant Transcription Factor Database
  • DATF Arabidopsis thaliana transcription factor database
  • EPD - Eukaryotic Promoter Database at EMBL, Heidelberg
  • dbTSS - database of Transcriptions Start Sites
  • Jaspar - The high-quality transcription factor binding profile database
  • PLACE - Database of Plant Cis-acting Regulatory DNA Elements
  • PlantCare - a Plant Promoters database
  • PlantPromDB - A Database of Plant Promoter Sequences
  • SCPD - the Promoter Database of Saccharomyces cerevisiae
  • TFD - the IFTI-MIRAGE website
  • TransFac - Gene Regulation
  • TRED - Transcriptional Regulatory Element Database
  • TRRD - Transcription Regulatory Regions Database
  • Dragon TF Integrator
  • cisRED database holds conserved sequence motifs identified by genome scale motif discovery
  • Rel/NF-kappaB target genes


    Phylogenetic Footprinting

  • Confac - Conserved Transcription Factor Binding Site Finder
  • Conreal - CONserved Regulatory Elements anchored ALignment
  • Consite - Explore transcription factor binding sites shared by two genomic sequences
  • Footprinter - Looks for motifs in a set of conserved sequences, based on sequences and the phylogenetic tree that connects them.
  • Phylofoot - Tools for phylogenetic footprinting purposes
  • PROMH - Search for promoters/functional motifs
  • rVista - v2.0


    Promoters in Groups of Genes

  • Alignace - AlignACE HomePage
  • Bindgene - A DNA Binding Site Searcher
  • Consensus
  • CREME - Cis-REgulatory Module Explorer 2.0
  • Gibbs motif sampler
  • MEME - The MEME/MAST System
  • MotifSampler - finds motifs in groups of sequences, and provides background models for cleaner predictions.
  • OTFBS - Over-represented Transcription Factor Binding Site Prediction Tool
  • PRIMA - a software for promoter analysis
  • PROMO - ALGGEN's Home Page (under research)
  • Reduce - Bussemaker Lab - Columbia University
  • R-Motif - Motif Analysis Workbench
  • RSAT - Regulatory Sequence Analysis Tools
  • Trafac - UC/CHMC TraFaC Homology Server
  • Vista - Tools for Comparative Genomics
  • Promoter Express
  • Weeder
  • Toucan
  • Creme
  • Athamap
  • MotifMogul
  • Improbizer
  • CRSD
  • Credo
  • MotifViz
  • GSEA - Gene Set Enrichment Analysis
  • Carrie
  • WebMotif
  • TFME


    Promoter Search Tools

  • Audic - Self-identification of coding regions in microbial genomes
  • CorePromoter - Human Core-Promoter Prediction Program
  • Dragon Promoter Finder
  • Eponine - Transcription Start Site finder
  • Gene Regulation Tools - (transfac search, Match, Patsearch,etc....)
  • McPromoter - The Markov Chain Promoter Prediction Server
  • NNPP - Prokaryotic promoter prediction at BCM
  • PromFD - (download)
  • PromFind - (download)
  • Promoter2.0 - Prediction server at CBS
  • PromoterInspector - Prediction of promoter regions in mammalian genomic sequences
  • Promoter Prediction - (Eukaryote + Prokaryote) by Neural Network at LBNL
  • PromoterScan 2 - predicts putative eukaryotic Pol II promoter sequences
  • Regulatory Sequence Analysis Tools
  • rVISTA - for comparative sequence-based discovery of functional transcription factor binding sites
  • Self-identification - of coding regions in microbial genomes
  • SignalScan
  • SoftBerry tools - for gene regulation and promoter search
  • Zhang Lab Tools - Promoter tools and databases for Human, Drosophila, C. Elegans, Arabidopsis, Yeast
  • Zlab - many tools for gene regulation


    Transcription Binding Tools

  • ALIBABA - predicts transcription factor binding sites by constructing matrices on the fly from TRANSFAC
  • Cister - Cis-element Cluster Finder
  • COMPEL - database on composite regulatory elements affecting gene transcription in eukaryotes
  • F-Match, Patch (PatSearch), Match....(Transfac 6.0) - programs links
  • MatInspector - find binding sites for transcription factors, at the GenomatixSuite, Germany
  • PLACE - a database of Plant Cis-acting Regulatory DNA Elements
  • RSA-tools - Regulatory Sequence Analysis tools - Search a pattern (string description) within all upstream or downstream regions of a genome
  • TESS - Predicting Transcription factors binding sites at CBIL, USA
  • TFSEARCH - searching Transcription Factor Binding Sites, Japan
  • Tfsitescan - at IFTI
  • TRANSFAC - a database on eukaryotic cis-acting regulatory DNA elements and trans-acting factors


    Transcription Start Site Prediction

  • DBTSS - Database of Transcriptional Start Sites
  • Dragon Gene Start Finder
  • Eponine - Transcription Start Site finder
  • FIE2 - Five-end Infromation Extraction v.2
  • FirstEF - first-exon and promoter prediction program for human DNA
  • PromoSer - Human, Mouse and Rat promoter extraction service

  • TransFind Predicting transcriptional regulators for gene sets


    Transcriptuion Terminator

  • TransTermHP finds rho-independent transcription terminators in bacterial genomes


    Prokaryote Promoters

  • Sigma70
  • Sigma54
  • Sigma 54
  • Dbtbs
  • MicrobesOnline
  • Prodoric
  • Prom EC
  • Promscan
  • Softberry
  • Ribex
  • RegulonDB
  • TractorDB
  • RSAT