Bioinformatics Links Directory - Contents tagged as 'transcription factors'

MONKEY

Mon, 13 May 2013 10:00:19 -0400

MONKEY is a set of programs designed to search alignments of non-coding DNA sequence for matches to matrices representing the sequence specificity of transcription factors.

CisRegTest

Fri, 17 May 2013 06:30:11 -0400

Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites.

MAPPER2 Database

Sun, 12 May 2013 07:30:18 -0400

The MAPPER Database contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream sequences of genes from the human, mouse and D.melanogaster genomes.

GBrowse

Fri, 17 May 2013 09:20:23 -0400

GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.

SISSRs

Fri, 17 May 2013 03:10:17 -0400

SISSRs (Site Identification from Short Sequence Reads), an algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments.

Filamentous Fungal Gene Expression Database (FFGED)

Sun, 12 May 2013 06:10:21 -0400

The filamentous fungal gene expression database (FFGED) is a user-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. FFGED functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, and correlating diverse gene expression levels under multiple experimental designs within different experiments.

CENTDIST

Tue, 14 May 2013 21:10:15 -0400

CENTDIST is a co-motif scanning program to identify co-transcription factors. CENTDIST ranks co-transcription factors based on their distribution around CHIP-seq peaks.

ChIP-Array

Thu, 09 May 2013 02:20:51 -0400

ChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.

Genome Surveyor

Fri, 17 May 2013 11:40:12 -0400

Genome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.

mirConnX

Thu, 16 May 2013 07:10:17 -0400

mirConnX is a web server for inferring, displaying and parsing mRNA and microRNA gene regulatory networks. mirConnX combines sequence information with gene expression data analysis to create a disease specific, genome wide regulatory network. Only supports human and mouse.

PRI-CAT

Sat, 11 May 2013 04:40:40 -0400

PRI-CAT is a web-based workflow tool for the management and analysis of plant ChIP-seq experiments, with focus on Arabidopsis. Secondary analysis can be performed with the aid of GALAXY.

REDfly

Fri, 03 May 2013 22:40:42 -0400

The REDfly database of Drosophila transcriptional cis-regulatory elements provides experimentally validated cis-regulatory modules and transcription factor binding sites. The user interface is designed for access by both causal and power users and is intended as a tool for facilitating computational as well as experimental studies of transcriptional regulation.

TcoF-DB

Wed, 15 May 2013 09:50:18 -0400

TcoF is a database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions (transcription factors) and proteins involved in the regulation of transcription in humans by interacting with transcription factors and not binding to regulatory DNA regions (transcription co-factors). Proteins can be searched by a variety of identifiers or predefined sets of proteins can be viewed.

YEASTRACT

Fri, 17 May 2013 15:00:14 -0400

The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) is a curated repository of regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. EASTRACT allows the identification of documented or potential transcription regulators of a given gene and of documented or potential regulons for each transcription factor. It also renders possible the comparison between DNA motifs and the transcription factor binding sites described in the literature. YEASTRACT provides a set of queries to search and retrieve important biological information from the gathered data and to predict transcription regulation networks in yeast from data emerging from gene-by-gene analysis or global approaches.

DroID

Thu, 16 May 2013 22:50:18 -0400

DroID, the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and experimentally detected protein-protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are annotated with experimental details and periodically updated confidence scores. The database now includes transcription factor-gene and regulatory RNA-gene interactions. Orthologous gene mappings of Drosophila genes to other organisms are also available to facilitate finding interactions based on gene names and identifiers for a number of common model organisms and humans.

YPA

Thu, 16 May 2013 09:40:23 -0400

The Yeast Promoter Atlas (YPA) database collects promoter features in Saccharomyces cerevisiae. YPA integrates nine kinds of promoter features including promoter sequences, genes' transcription boundaries-transcription start sites (TSSs), five prime untranslated regions (5'-UTRs) and three prime untranslated regions (3'UTRs), TATA boxes, transcription factor binding sites (TFBSs), nucleosome occupancy, DNA bendability, transcription factor (TF) binding, TF knockout expression and TF-TF physical interaction. In YPA, various promoter features can be accessed in a centralized and organized platform.

RegulonDB

Wed, 15 May 2013 10:20:34 -0400

RegulonDB is a reference database of Escherichia coli K-12. Transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. In addition to data from the literature, we have incorporated our own information on transcription start sites (TSSs) and transcriptional units (TUs), obtained by using high-throughput whole-genome sequencing technologies. A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format.

AGRIS

Wed, 15 May 2013 23:10:40 -0400

The Arabidopsis Gene Regulatory Information Server (AGRIS) provides a comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively.

FANTOM

Thu, 16 May 2013 08:00:21 -0400

The Functional Annotation Of the Mammalian Genome (FANTOM) is a database for the transcriptional network that regulates macrophage differentiation. Data comes from cap analysis of gene expression (CAGE), sequencing mRNA 5'-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors.

PlantTFDB 2.0

Tue, 14 May 2013 04:40:27 -0400

The PlantTFDB 2.0 plant transcription factor (TF) database contains detailed annotation including general information, domain feature, gene ontology, expression pattern and ortholog groups, as well as cross references to various databases and literature citations for these TFs. Multiple sequence alignments and phylogenetic trees for each family can be shown as Weblogo pictures or downloaded as text files.

FlyFactorSurvey

Fri, 17 May 2013 02:00:21 -0400

FlyFactorSurvey is a database of DNA binding specificities for Drosophila transcription factors (TFs) determined using the bacterial one-hybrid system. The database provides to recognition motifs and position weight matrices for TFs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome.

PlnTFDB

Tue, 14 May 2013 04:30:15 -0400

The Plant Transcription Factor Database (PlnTFDB) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and annotated. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.

HLungDB

Fri, 17 May 2013 06:30:11 -0400

The human lung cancer database (HLungDB) is a database with the integration of the lung cancer-related genes, proteins and miRNAs together with the corresponding clinical information. Currently, we have collected 2585 genes and 212 miRNA with the experimental evidences involved in the different stages of lung carcinogenesis through text mining. The results from analysis of transcription factor-binding motifs, the promoters and the SNP sites for each gene are also included. Genes with epigenetic regulation were also included.

WormBase

Tue, 14 May 2013 10:00:07 -0400

WormBase is a data repository for nematode biology. WormBase has expanded to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes.

FlyTF

Wed, 15 May 2013 21:50:21 -0400

FlyTF is a database of computationally predicted and/or experimentally verified site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. This database contains information on the manual curation of 1052 FlyBase identifiers, which are putative site-specific transcription factors, based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database.

miRGen

Wed, 15 May 2013 23:10:45 -0400

miRGen 2.0 is a database that aims to provide comprehensive information about the position of human and mouse microRNA coding transcripts and their regulation by transcription factors, including a unique compilation of both predicted and experimentally supported data. Expression profiles of microRNAs in several tissues and cell lines, single nucleotide polymorphism locations, microRNA target prediction on protein coding genes and mapping of miRNA targets of co-regulated miRNAs on biological pathways are also integrated into the database and user interface.

TransmiR

Wed, 15 May 2013 10:20:08 -0400

The TF-miRNA regulatory database (TransmiR) contains transcription factors and miRNAs along with regulatory pairs. References to the published literature (PubMed ID) information about the organism in which the relationship was found, whether the TFs and miRNAs are involved with tumors, miRNA function annotation and miRNA-associated disease annotation are also included. TransmiR provides a user-friendly interface by which interested parties can easily retrieve TF-miRNA regulatory pairs by searching for either a miRNA or a TF.

RegPrecise

Mon, 13 May 2013 14:40:24 -0400

The RegPrecise database was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. The reconstructed regulons include transcription factors, their cognate DNA motifs and regulated genes/operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. Another section in the database represents the results of accurate regulon propagation to the closely related genomes.

JASPAR

Fri, 17 May 2013 16:00:07 -0400

JASPAR is an open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. The database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family.

REDfly

Fri, 17 May 2013 01:50:26 -0400

Regulatory Element Database for Drosophila (REDfly) is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs). REDfly seeks to include all experimentally verified fly CRMs along with their DNA sequence, their associated genes, and the expression patterns they direct.

ORegAnno

Fri, 17 May 2013 06:10:19 -0400

The Open REGulatory ANNOtation database (ORegAnno) is a collection of literature-curated regulatory regions, transcription factor binding sites (TFBS) and regulatory mutations.

PlnTFDB

Wed, 15 May 2013 09:20:18 -0400

Plant Transcription Factor Database (PlantTFDB) is database that attempts to identify a comprehensive set of plant genes coding for transcription factors. A web interface to the database allows users to browse by species, search using a sequence identifier, or query using BLAST.

rSNP_Guide

Tue, 07 May 2013 02:10:20 -0400

a system of databases documenting the influence of mutations in regulatory gene regions

FANTOM - Functional Annotation of Mouse

Wed, 15 May 2013 16:30:35 -0400

Functional annotations for RIKEN full-length cDNA clones.

WormBase

Thu, 16 May 2013 04:40:26 -0400

Repository of mapping, sequencing and phenotypic information about C. elegans and C. briggsae.

DCODE.ORG

Wed, 15 May 2013 17:50:35 -0400

The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CREME, and the ECR Browser.

PathGuide

Tue, 14 May 2013 22:20:24 -0400

The PathGuide - Pathway Resource List (PRL) is a database of 250+ links to resources for protein-protein interactions, metabolic and signalling pathways, transcription factor and genetic interaction networks, pathway diagrams, protein sequences, and protein-compound interactions.

Phyloscan

Fri, 17 May 2013 13:10:18 -0400

Phyloscan is a web server that locates transcription regulating binding sites by exploiting binding site evolutionary conservation and repeats in promoter regions. Mixed aligned and unaligned sequence data may be used.

MEME Suite

Wed, 15 May 2013 12:50:23 -0400

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

Pscan

Tue, 14 May 2013 12:20:22 -0400

Pscan is a web server scans a set of sequences to find over-represented transcription factor binding site motifs within co-regulated or co-expressed genes.

ProteDNA

Thu, 16 May 2013 21:30:35 -0400

ProteDNA identifies the sequence-specific binding residues in a transcription factor, protein-DNA interaction.

SNPinfo

Thu, 16 May 2013 14:40:15 -0400

A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.

PAP

Wed, 15 May 2013 15:30:23 -0400

Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.

ZiFiT

Mon, 13 May 2013 13:30:14 -0400

ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences. ZiFiT has been updated to integrate additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database of engineered ZFPs, and direct query of NCBI BLAST servers for identification of potential off-target sites within a host genome.

WebMOTIFS

Fri, 17 May 2013 05:30:10 -0400

WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.

oPOSSUM

Fri, 17 May 2013 16:10:21 -0400

oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.

MoD Tools

Fri, 17 May 2013 15:10:07 -0400

Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences.

POXO

Tue, 14 May 2013 10:30:24 -0400

POXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes.

VOMBAT

Fri, 17 May 2013 14:50:12 -0400

VOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees.

iCR

Thu, 09 May 2013 16:20:17 -0400

Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.

Zinc Finger Tools

Fri, 17 May 2013 11:40:16 -0400

Zinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.

Match

Fri, 17 May 2013 08:50:38 -0400

Match is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match.

SiteSeer

Thu, 16 May 2013 10:50:12 -0400

SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.

REDUCE

Fri, 17 May 2013 08:00:12 -0400

REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.

NXSensor

Thu, 16 May 2013 21:10:11 -0400

Nucleosome eXclusion Sensor (NXSensor) finds potential nucleosome-free regions of DNA sequences. NXSensor can be used to assess the likelihood of nucleosome formation in regions involved in gene regulation and other aspects of chromatin function.

ALGGEN

Thu, 16 May 2013 01:00:44 -0400

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

PatSearch

Tue, 14 May 2013 03:40:32 -0400

PatSearch is a pattern matcher that is able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices.

RSAT

Fri, 17 May 2013 01:40:25 -0400

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

YMF 3.0

Sun, 12 May 2013 20:50:23 -0400

YMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs. Multiple organisms are supported including human, yeast, worm, plants, and microbes.

T-Reg Comparator

Thu, 16 May 2013 15:10:25 -0400

T-Reg Comparator is a tool for the analysis of transcriptional regulation that allows you to compare a set of position weight matrices (PWM) against the T-Reg database (a collection of PWMs built from Transfac and Jaspar).

SynoR

Wed, 15 May 2013 14:20:18 -0400

SynoR searches vertebrate genomes for synonymous regulatory elements.

VisANT

Mon, 13 May 2013 20:00:07 -0400

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

POCO

Fri, 17 May 2013 14:10:08 -0400

POCO searches a set of promoters from co-expressed genes for nucleotide patterns that are over-represented.

E-RNAi

Thu, 16 May 2013 06:00:49 -0400

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

Footer

Tue, 14 May 2013 13:40:18 -0400

Footer is a tool for identifying highly-probable binding sites of known transcription factors using phylogenetic footprinting principles to analyse two homologous DNA sequences.

VAMPIRE

Sun, 12 May 2013 07:20:33 -0400

VAMPIRE is a collection of Java tools designed to perform Bayesian statistical analysis of gene expression array data.

P-Match

Thu, 16 May 2013 18:20:32 -0400

P-Match is a transcription factor binding site identification tool that increases its accuracy by combining weight matrix and pattern matching approaches. Registration at the site is free and is required to use P-Match.

HHpred

Fri, 17 May 2013 02:20:34 -0400

Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.

zPicture and multi-zPicture

Wed, 15 May 2013 10:40:22 -0400

zPicture (pairwise alignment) and multi-zPicture (multiple alignment) are web-based sequence alignment tools based on the blastz alignment program. Alignments from zPicture can be automatically submitted to rVista.

ECR Browser

Sun, 12 May 2013 01:20:33 -0400

The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.

TFBScluster

Fri, 17 May 2013 04:00:14 -0400

TFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized.

CREME

Wed, 15 May 2013 11:50:18 -0400

CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.

PromoterPlot

Fri, 17 May 2013 05:40:19 -0400

PromoterPlot takes the output from a TransFac search as input, and finds similarities between groups of promoters in an attempt to simplify the results of transcription factor searches. FASTA/Affymetrix IDs can also be used as input for a local installation of the tool.

Pathway Hunter Tool

Tue, 14 May 2013 16:30:17 -0400

Pathway Hunter Tool (PHT) uses shortest path analysis to reconstruct and visualize biochemical pathways. The user can find the shortest path between two metabolites, or find all reachable products or educts for a given metabolite.

rVISTA

Fri, 10 May 2013 19:20:16 -0400

Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis.

POBO

Tue, 14 May 2013 22:40:19 -0400

POBO is a tool to summarize, verify and screen predetermined cis-element motifs from a set of sequences. POBO reports the results in as understandable format as possible for biologists.

MDscan

Wed, 15 May 2013 06:40:16 -0400

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.

SITECON

Thu, 16 May 2013 01:10:28 -0400

Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites.

Web Weeder

Fri, 17 May 2013 14:40:41 -0400

Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parameters and output a summary.

MotifViz

Fri, 17 May 2013 16:20:09 -0400

MotifViz is a tool for detecting overrepresented transcription factor binding motifs. Four motif discovery programs are accessible from the MotifViz web interface: Clover, Rover, Motifish and Possum.

PredictRegulon

Mon, 13 May 2013 00:50:23 -0400

PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. PredictRegulon reports back with predicted binding sites and downstream co-regulated genes.

JASPAR

Wed, 15 May 2013 14:00:20 -0400

JASPAR is a non-redundant, curated collection of transcription factor binding profiles. Each profile is generated from published, experimentally defined eukaryotic transcription factor binding sites.

TOUCAN 2

Thu, 16 May 2013 12:40:14 -0400

TOUCAN 2 is a regulatory sequence analysis workbench for Metazoan sequences, directly linked with the Ensembl database and implementing SOAP clients for diverse alignment and motif detection algorithms.

DRTF

Sat, 11 May 2013 23:30:28 -0400

Database of Rice Transcription Factor (DRTF) is a collection of known and predicted transcription factors from japonica and indica rice genomes.

Drosophila DNase I footprint database

Thu, 16 May 2013 19:20:27 -0400

Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.

DiRE

Fri, 17 May 2013 13:30:43 -0400

A web server for predicting distant (outside of proximal promoter regions) regulatory elements (DiRE) in higher eukaryotic genomces using gene co-expression data, comparative genomics as well as transcription factor binding site information. DiRE allows users to start analysis with raw microarray expression data.

DATF

Thu, 16 May 2013 10:50:33 -0400

The Database of Arabidopsis Transcription Factors (DATF) contains information of more than 1800 known and predicted transcription factors for Arabidopsis.

CRSD

Fri, 17 May 2013 14:00:21 -0400

Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).

Consite

Sun, 12 May 2013 20:10:16 -0400

Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.

CONREAL

Thu, 16 May 2013 16:00:36 -0400

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

CompareProspector

Mon, 13 May 2013 19:00:12 -0400

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.

CMA

Mon, 13 May 2013 05:40:14 -0400

Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.

Cluster Buster

Wed, 15 May 2013 10:40:26 -0400

Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.

CEAS

Thu, 16 May 2013 10:20:22 -0400

Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.

FatiGOplus

Thu, 16 May 2013 09:50:35 -0400

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

CARRIE

Fri, 17 May 2013 02:40:38 -0400

Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.

TFM-Explorer

Fri, 17 May 2013 07:50:20 -0400

TFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.

BioProspector

Sun, 12 May 2013 20:20:10 -0400

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.

BioMet Toolbox

Thu, 16 May 2013 16:50:33 -0400

The BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.

BioBayesNet

Wed, 15 May 2013 15:10:21 -0400

BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.

BEARR

Thu, 16 May 2013 14:40:30 -0400

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

ARGO

Wed, 15 May 2013 18:00:39 -0400

ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.

ACT

Thu, 16 May 2013 17:50:15 -0400

Arabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis.

@TOME-2

Fri, 17 May 2013 00:20:22 -0400

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.