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A Suite of Web-based Programs to Search for Transcriptional Regulatory Motifs
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| Identify potential transcription factors binding sites.
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ABS -- a database of Annotated regulatory Binding Sites from orthologous promoters
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| Search for known binding sites in promoters of orthologous vertebrate genes.
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ACTIVITY -- A distributed and intelligent database for the activities of the functional sites in DNA and RNA.
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| Search for activities of the functional sites in DNA and RNA.
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ARGO -- a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters
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| Detect sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of the eukaryotic genes.
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ATTED-II -- a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis
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| Search for information on predicted Arabidopsis thaliana trans-factor and cis-element and co-regulated gene relationships based on microarray data. |
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Agris -- The Arabidopsis Gene Regulatory Information Server
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| Search for comprehensive information on Arabidopsis promoter sequences, transcription factors and their target genes. |
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AraC-XylS database -- a family of positive transcriptional regulators in bacteria
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| Search information about a family of positive transcriptional regulators broadly distributed in bacteria.
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AthaMap -- integrating transcriptional and post-transcriptional data
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| Generate a map of cis-regulatory elements for the Arabidopsis thaliana genome. |
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BEARR -- Batch Extraction and Analysis of cis-Regulatory Regions
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| Identify and analyze cis-elements from microarray data.
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BacTregulators -- A database of transcriptional regulators in prokaryotes
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| Search for sequences and other information about prokaryotic transcriptional regulators. |
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CAGE Basic/Analysis Databases -- the CAGE resource for comprehensive promoter analysis
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| Search for comprehensive Cap-analysis gene expression (CAGE) Basic data and Analysis results. |
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CARRIE -- Computational Ascertainment of Regulatory Relationships Inferred from Expression
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| Analyze microarray and promoter data to infer transcriptional regulatory network. |
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CEAS -- cis-regulatory element annotation system
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| Analyze data from high throughput ChIP-chip experiments to annotate cis-regulatory elements.
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CONREAL web server -- identification and visualization of conserved transcription factor binding sites
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| Identify and visualize conserved transcription factor bindings sites in orthologous promoters.
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CORG -- A database for COmparative Regulatory Genomics
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| Delineate conserved non-coding blocks from upstream regions of putative orthologous gene pairs from man, mouse, rat, fugu, Mus musculus, Danio rerio, and zebrafish. |
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COXPRESdb -- a database of coexpressed gene networks in mammals
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| Find coexpressed gene lists and networks in human and mouse.
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CREME -- Cis-Regulatory Module Explorer for the Human Genome
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| Identify and visualize cis-regulatory modules in the promoter regions of a given set of potentially co-regulated genes in human genome.
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CRSD -- a comprehensive web server for composite regulatory signature discovery
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| Conduct multi-facet analysis of composite regulatory signature by transcription factors and microRNA on gene expression.
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CTCFBSDB -- a CTCF-binding site database for characterization of vertebrate genomic insulators
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| A database that characterize experimentally identified and computationally predicted CTCF-binding sites.
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CisMols Analyzer -- identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes
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| Analyze and identify maximal numbers of compositionally similar and phylogenetically conserved cis-regulatory element clusters from a list of user-selected genes.
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Cluster-Buster -- finding dense clusters of motifs in DNA sequences
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| Find clusters of pre-specified motifs in nucleotide sequences.
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Composite Module Analyst -- identification of transcription factor binding site combinations using genetic algorithm
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| Identify promoter-enhancer models based on the composition of transcription factor (TF) binding sites and their pairs.
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Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription
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| Perform automated comprehensive analyses of promoter regulatory motifs and the effect they exert on mRNA expression profiles.
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ConSite -- Web-based Prediction of Regulatory Elements using Cross-species Comparison
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| Find cis-regulatory elements in genomic sequences.
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ConTra -- conserved transcription factor binding sites
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| A promoter alignment analysis tool for identification of transcription factor binding sites across species.
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DATF -- a database of Arabidopsis transcription factors
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| Search for information on Arabidopsis transcription factors. |
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DBD -- a transcription factor prediction database
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| A database of predicted sequence-specific DNA-binding transcription factors (TFs) for all publicly available proteomes.
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DBD-Hunter -- DNA-binding Domain Hunter
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| A knowledge-based method for the prediction of DNA-protein interactions.
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DBTBS -- Bacillus transcriptional regulation database
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| Search for information on Bacillus transcription factors and conduct comparative genomics study on TFs.
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DBTGR -- a database of tunicate promoters and their regulatory elements
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| Search for information on tunicate promoters and regulatory elements. |
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DBTSS -- a database of transcriptional start sites
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| Search for transcriptional starting sites in human and mouse genomes; conduct comparative promoter analysis.
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DPInteract -- A comprehensive library of binding sites for E. coli DNA-binding proteins
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| Search for experimentally determined DNA binding proteins and their binding sites over the complete E. coli K12 genome.
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Dcode.org anthology of comparative genomic tools
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| Demarcate functional regions in genomic DNA sequences using a list of tools. |
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DiRE -- distant regulatory elements
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| Identify distant regulatory elements of co-expressed genes.
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DoOP -- Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants
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| Search and analyze eukaryotic promoter sequences in orthologous genes.
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Dragon ERE Finder version 2 -- a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes
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| Identify estrogen response elements (EREs) in genomic DNA.
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Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes
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| Predict gene start sites in mammalian genomes.
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Dragon TF Association Miner -- A System for Exploring Transcription Factor Associations Through Text-mining
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| Mine PubMed documents for potential functional association of transcription factors (TFs) with terms from Gene Ontology (GO) and with diseases.
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EPConDB -- Endocrine pancreas consortium database
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| Search for information on genes expressed in pancreas. |
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EPD -- eukaryotic promoter database
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| Search for annotated information on eukaryotic promoters and conduct comparative promoter analysis.
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ERTargetDB -- an integral information resource of transcription regulation of estrogen receptor target genes
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| Search for comprehensive information on transcription regulation of estrogen receptor target genes.
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ExtraTrain -- A database of Extragenic regions and transcriptional regulators in bacteria and archaea
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| Search for extragenic regions in over 230 bacterial and Archaeal genomes.
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FIE2 -- a program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes
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| Identify and extract nucleotide sequence around the start of genes (promoter region) and their translation initiation site (TIS).
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FOOTER -- a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
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| Analyze homologous mammalian promoter sequences in order to identify transcriptional DNA regulatory signals.
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FootPrinter3 -- phylogenetic footprinting in partially alignable sequences
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| Discover regulatory elements in a set of homologous regulatory regions.
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GenomeTrafac -- a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
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| Use comparative genomics approach to characterize gene models and identify putative cis-regulatory regions of RefSeq Gene Orthologs.
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Gibbs Recursive Sampler -- finding transcription factor binding sites
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| Locate multiple transcription factor binding sites for multiple transcription factors simultaneously in unaligned DNA sequences that may be heterogeneous in DNA composition.
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HTPSELEX — a database of high-throughput SELEX libraries for transcription factor binding sites
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| Search for transcription factor binding sites sequences obtained with SELEX and high-throughput SELEX method.
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HemoPDB -- hematopoiesis promoter database
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| Search for transcription factors involved in the human hematopoietic development and their binding sites in the target gene promoters.
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INCLUSive -- a web portal and service registry for microarray and regulatory sequence analysis
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| Use a suite of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements. |
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ITFP -- integrated transcription factor platform
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| An integrated platform of mammalian transcription factors.
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Identification of patterns in biological sequences at the ALGGEN server -- PROMO and MALGEN
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| Predict of transcription factor binding sites or visualize sequence correspondences among long DNA sequences.
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Identifying synonymous regulatory elements in vertebrate genomes
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| Scan vertebrate genomes for evolutionary conserved modules of transcription factor binding sites.
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InsulatorDB -- A Vertebrate Insulator Database
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| Search for comprehensive information of known insulator elements in the vertebrates.
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JASPAR -- database for eukaryotic transcription factor binding profiles
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| Search for transcription factor binding site profiles for multicellular eukaryotes.
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LICORN -- learning cooperative regulation networks from gene expression data
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| Infer transcriptional regulation relationships from RNA expression values.
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LymphTF DB
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| A portal of information regarding transcription factor (TF) activity in the developing B and T cells (lymphocytes) in the mouse. |
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MATCH -- a tool for searching transcription factor binding sites in DNA sequences
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| Search potential binding sites for transcription factors (TF binding sites) nucleotide sequences.
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MEME -- discovering and analyzing DNA and protein sequence motifs
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| Find sequence patterns in DNA and protein sequences. |
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MOPAT -- motif pair tree
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| A graph-based method to predict recurrent cis-regulatory modules from known motifs.
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MPromDb -- an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data
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| Search for annotated information on mammalian promoters.
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MSCAN -- Identification of Functional Clusters of Transcription Factor Binding Sites
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| Identify functional transcription factor binding sites in genomic sequences.
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MYBS -- Mining Yeast Binding Sites
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| A comprehensive web server for mining transcription factor binding sites in yeast.
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MachiBase -- a Drosophila melanogaster 5'-end mRNA transcription database
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| Find information about fruit fly mRNA transcription during development.
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Melina II -- a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
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| A web-based tool for promoter analysis.
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MicroFootPrinter -- a tool for phylogenetic footprinting in prokaryotic genomes
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| Identify motifs that are well conserved across the cis-regulatory regions of these homologous genes in microorganisms.
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MoD Tools -- regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
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| Discover regulatory motifs in DNA sequences from co-regulated or homologous genes.
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MotifViz -- An Analysis and Visualization Tool for Motif Discovery
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| Identify functional sites (cis-elements) in DNA sequences.
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Myc Cancer Database
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| Find information on Myc target genes, the role of Myc in human cancers, and proteins that interact with the Myc transcription factors |
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NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors
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| Find nucleosome exclusion sequences and analyze their accessibility to binding factors. |
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OMGProm -- a database of orthologous mammalian gene promoters
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| Search for annotated orthologous mammalian gene promoter sequences.
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ORegAnno -- an open-access community-driven resource for regulatory annotation
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| Find experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants using this open-source, open-access database and literature curation system for community-based annotation.
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Osteo-Promoter Database (OPD) -- promoter analysis in skeletal cells
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| Search for information on gene expressed in skeletal cells and their promoter sequences. |
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P-Match -- transcription factor binding site search by combining patterns and weight matrices
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| Identify transcription factor (TF) binding sites in DNA sequences.
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PAP -- Promoter Analysis Pipeline
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| A comprehensive workbench for mammalian transcriptional regulatory sequence analysis.
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PAZAR -- Transcription Factor and Regulatory Sequence Annotation Database
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| Find information about gene regulation.
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PLACE -- Plant cis-acting regulatory DNA elements
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| Search for documented motifs found in plant cis-acting regulatory DNA elements.
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POBO -- Transcription Factor Binding Site Verification with Bootstrapping
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| Verify putative regulatory motifs.
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POCO -- discovery of regulatory patterns from promoters of oppositely expressed gene sets
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| Detect transcription factor binding sites in promoters of co-regulated genes.
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POXO -- a web-enabled tool series to discover transcription factor binding sites
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| Discover transcription factor binding sites from co-expressed genes.
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PRODORIC -- Prokaryotic database of gene regulation
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| Search for curated information on prokaryotic gene expression and regulatory networks.
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PReMod -- a database of genome-wide mammalian cis-regulatory module predictions
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| Conduct genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes.
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PTM-Switchboard -- Post-Translational Modifications of Transcription Factors Database
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| Find information about 'molecular switchboards'.
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PlantCARE -- A database of plant cis-acting elements
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| Search for information on plant cis-acting regulatory elements, transcription sites, enhancers and repressors.
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PlantProm -- A database of plant promoter sequences
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| Search for promoter sequences for RNA polymerase II with experimentally determined transcription start sites from various plant species.
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PredictRegulon -- A Web Server for the Prediction of the Regulatory Protein Binding Sites and Operons in Prokaryote Genomes
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| Predict the potential binding sites and its target operons for a given regulatory protein in prokaryotic genomes.
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ProTISA -- a comprehensive resource for translation initiation site annotation in prokaryotic genomes
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| Find confirmed translation initiation sites (TISs) for prokaryotic genomes.
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PromAn -- an integrated knowledge-based web server dedicated to promoter analysis
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| Analyze promoter sequences to locate transcription start sites (TSS) and Transcription factor binding sites (TFBSs).
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PromEC -- A database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites
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| Search for information on E. coli mRNA promoter sequences and transcriptional start sites.
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PromH -- promoters identification using orthologous genomic sequences
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| Predict promoter and transcription starting site (TSS) using orthologous sequences in eukaryotic genomes.
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PromoSer -- a large-scale mammalian promoter and transcription start site identification service
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| Extract user specified regions around the transcription start site of all annotated human, mouse or rat genes.
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PromoterPlot -- a graphical display of promoter similarities by pattern recognition
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| Visualize sequence similarities among a group of promoters.
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REDUCE -- an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data
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| Use motif-based regression method to analyze microarray data. |
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RSAT -- Regulatory Sequence Analysis Tools
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| Detect regulatory elements in non-coding sequences.
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ReXSpecies -- Regulation across species
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| A tool for the analysis of the evolution of gene regulation across species.
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RegTransBase —- a database of regulatory sequences and interactions in a wide range of prokaryotic genomes
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| Search for manually curated regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary.
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RibEx -- a web server for locating riboswitches and other conserved bacterial regulatory elements
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| Search sequences of known and predicted riboswitches and other conserved bacterial regulatory elements. |
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SCPD -- Saccharomyces cerevisiae promoter database
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| Search for information on promoter and regulatory elements in yeast genome. |
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SELEX_DB -- A database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data
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| Search for information on both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for these oligomers recognition.
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SITECON -- Detecting Conservative Conformational and Physicochemical Properties in Transcription Factor Binding Site Alignments and for Site Recognition
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| Search for DNA-binding sites and conserved local DNA conformation within the binding regions.
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STAMP: a web tool for exploring DNA-binding motif similarities.
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| Search DNA motifs against databases of known motifs (JASPAR, TRANSFAC etc.) |
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SeqVISTA -- An Integrated Computational Tools for Studying Transcriptional Regulation
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| Study transcriptional regulation using integrated of gene regulation analysis software.
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Signal search analysis server
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| Analyze nucleic acid sequence motifs that are positionally correlated with a functional site such as a transcription initiation site for instance.
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SiteSeer -- visualization and analysis of transcription factor binding sites in nucleotide sequences
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| Visualize mapped transcription factor binding sites in the upstream regions of either single or grouped eukaryotic genes.
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Stubb -- a program for discovery and analysis of cis-regulatory modules
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| Find significant clusters of transcription factor binding sites over long genomic sequences.
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Swiss EMBnet node web server
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| Use a collection of bioinformatics tools at this portal site. |
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SwissRegulon -- a database of genome-wide annotations of regulatory sites
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| Search for genome-wide annotations of regulatory sites in yeast and prokaryotes genomes.
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T-Reg Comparator -- an analysis tool for the comparison of position weight matrices
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| 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.
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TESS -- Transcription Element Search System
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| Search or predict transcription factor binding sites in DNA sequences.
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TFBScluster web server for the identification of mammalian composite regulatory elements
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| Search and characterize composite regulatory elements in mammalian genomes.
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TFCONES -- Transcription Factor Genes & Associated COnserved Noncoding ElementS
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| A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements.
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TICO -- a tool for postprocessing the predictions of prokaryotic translation initiation sites
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| Predict prokaryotic translation initiation sites.
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TOUCAN 2 -- the all-inclusive open source workbench for regulatory sequence analysis
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| Analyze regulatory sequences in metazoan genomes.
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TRACTOR_DB -- A database of regulatory networks in gamma-proteobacterial genomes
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| Search for computationally predicted transcription factors binding sites in gamma-proteobacterial genomes.
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TRANSCompel® 6 -- A database on composite regulatory elements in eukaryotic genes
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| Search for information about composite elements - the basic structures of combinatorial gene regulation in eukaryotes.
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TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes
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| Search for comprehensive information on eukaryotic transcription factors.
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TRANSPATH ® -- An integrated database on signal transduction and a tool for array analysis
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| Analyze and visualize gene regulatory networks that combines encyclopedic information on signal transduction pathway. |
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TRED -- A Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies
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| Search for annotated and comprehensive information about cis- and trans-regulatory elements in human, mouse and rat genomes.
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TRRD -- Transcription Regulatory Regions Database
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| Search for information on structural and functional organization of transcription regulatory regions of eukaryotic genes.
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Target Explorer -- an automated tool for the identification of new target genes for a specified set of transcription factors
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| Predict clusters of binding sites for transcription factors in the context information taken from genome annotations.
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The MAPPER database -- A multi-genome catalog of putative transcription factor binding sites
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| Search for putative transcription factor binding sites in multiple genomes (human, mouse and D. melanogaster).
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TiProD -- the Tissue-specific Promoter Database
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| Search for information about promoter sequences for tissue-specificity in human.
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TrSDB -- A Proteome Database of Transcription Factors
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| To search for proteomic information on eukaryotic transcription factors. |
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UniPROBE -- Universal PBM Resource for Oligonucleotide Binding Evaluation
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| Find information about DNA binding in proteins.
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VOMBAT -- prediction of transcription factor binding sites using variable order Bayesian trees
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| Predict transcription factor binding sites using variable order Bayesian trees.
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WEB-THERMODYN -- sequence analysis software for profiling DNA helical stability
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| Analyze DNA sequences and compute the DNA helical stability. |
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Weeder Web -- discovery of transcription factor binding sites in a set of sequences from co-regulated genes
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| Find novel motifs ( transcription factor binding sites ) conserved in a set of regulatory regions of related genes.
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WordSpy -- identifying transcription factor binding motifs by building a dictionary and learning a grammar
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| Identify transcription factor binding sites or other meaningful DNA motifs.
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YMF -- a program for discovery of novel transcription factor binding sites by statistical over-representation
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| Identify good candidates for such transcription factor binding sites by searching for statistically overrepresented motifs.
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Zinc Finger Tools -- custom DNA-binding domains for transcription factors and nucleases
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| Search and prediction Zinc Finger Protein binding sites.
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cisRED -- a database system for genome-scale computational discovery of regulatory elements
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| Search for conserved regulatory elements.
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dPattern -- Binding Site Discovery in Human Genome using a Discriminate Pattern Approach
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| Transcription factor binding site discovery in human genome using a discriminative pattern analysis.
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dbQSNP -- a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods
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| Search SNPs in human promoter regions. |
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iCR -- a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species
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| Identify binding sites conserved in multiple prokaryotes for a given transcription factor.
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jPREdictor -- a versatile tool for the prediction of cis-regulatory elements
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| Predict cis-regulatory elements based on short motifs (protein bindings sites on DNA).
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oPOSSUM -- integrated tools for analysis of regulatory motif over-representation
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| Detect over-represented transcription factor binding sites in the promoters of sets of genes.
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ooTFD -- Object-oriented Transcription Factors Database
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| Search for binding and interactions information of transcription factors. |
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rSNP_Guide -- A database system for analysis of transcription factor binding to DNA with variations
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| Investigate the influence of mutations in regulatory gene regions onto DNA interaction with nuclear proteins.
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rVISTA 2.0 -- Evolutionary Analysis of Transcription Factor Binding Sites
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| Analyze the regulatory potential of noncoding sequences.
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