LSCF Bioinformatics - 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

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