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 Server
  • 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
  • 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 at BioBase
  • TRED - Transcriptional Regulatory Element Database
  • TRRD - Transcription Regulatory Regions Database
  • cisRED database holds conserved sequence motifs identified by genome scale motif discovery
  • Rel/NF-kappaB target genesi

  • 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
  • PROMH - Search for promoters/functional motifs
  • rVista - v2.0

  • Promoters in Groups of Genes

  • AlignACE - a program which finds sequence elements conserved in a set of DNA sequences from Church lab
    Download program Here
  • 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 from Shamir's lab
  • PROMO - ALGGEN's Home Page (under research)
  • RSAT - Regulatory Sequence Analysis Toolsi
  • Trafac - UC/CHMC TraFaC Homology Server
  • Vista - Tools for Comparative Genomics
  • Toucan a workbench for regulatory sequence analysis on metazoan genomes
  • DiRE Distant Regulatory Elements
  • Athamap - a genome-wide map of potential transcription factor and small RNA binding sites in Arabidopsis thaliana
  • MotifMogul a web server that enables the analysis of multiple DNA sequences using sets of Position Weight Matrices
  • Improbizer searches for motifs in DNA or RNA sequences that occur with improbable frequency
  • MotifViz Motif Search and Visualization
  • GSEA - Gene Set Enrichment Analysis from BROAD institute
  • Carrie Computational Ascertainment of Regulatory Relationships (Inferred from Expression)
  • WebMotif from Fraenkel's lab
  • TFME - a software suite for identifying and analyzing transcription factor bindings sites

  • Promoter Search Tools

  • CorePromoter - Human Core-Promoter Prediction Program
  • NNPP Neural Network Promoter Prediction at Berkeley
  • Promoter2.0 - Prediction server at CBS
  • PromoterInspector - Prediction of promoter regions in mammalian genomic sequences
  • PromoterScan - predicts putative eukaryotic Pol II promoter sequences
  • Regulatory Sequence Analysis Tools
  • SignalScan - Find and list homologies of published signal sequences with the input DNA sequence
  • 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
  • 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
  • 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
  • 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

  • Dbtbs Transcription Factors Regulated Operons
  • MicrobesOnline
  • Prodoric a comprehensive database about gene regulation and gene expression in prokaryotes
  • Promscan
  • Softberry
  • Ribex
  • RegulonDB
  • TractorDB
  • RSAT