Search for potential transcription factor binding sites in your own sequences using TRANSFAC matrices; free for non-commercial use. - [Read more MatInspector]
Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles. - [Read more Consite]
The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from t - [Read more CONFAC]
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. - [Read more BioProspector]
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. - [Read more JASPAR]
MSCAN takes as input one or more DNA sequences and a set of transcription factor binding site profiles. It then detects clusters of the binding sites in the sequences. - [Read more MSCAN]
Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis. - [Read more rVISTA]
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 bot - [Read more BEARR]
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 re - [Read more CREME]
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 invol - [Read more CARRIE]
A server for the detection, comparison and verification of transcription factor binding site motifs in promoters. POBO bootstrap analysis applied to one or two clusters of co-regulated genes detects motifs under extreme levels of representation. - [Read more POBO]
The website of the Ohio State University Human Cancer Genetics Bioinformatics group. This site has many resources, including databases of promoters and transcription factors, software tools to predict potential P53 consensus binding sites and to predict - [Read more OSU Bioinformatics and Computational Biology]
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. - [Read more CompareProspector]
ACMES (Advanced Content Matching Engine for Sequences) is a server that can be used to search for short repeats (between 3 and 10 000 bases) across multiple species. Users can limit results of a search by keyword searches. - [Read more ACMES]
RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis. - [Read more Riboswitch finder]
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. - [Read more MDscan]
Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy. - [Read more Eponine]
Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use. - [Read more TRANSFAC]
First Exon Finder (FirstEF) is a 5' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree. - [Read more FirstEF]
Searchable literature network of human genes with tools for gene expression analysis. Choose from the free public service, or purchase the commercial package. - [Read more PubGene]
Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detail - [Read more IBM Bioinformatics and Pattern Discovery Group]
Database of protein families and domains defined from SwissProt database; consider also checking specific motif databases such as PhosphoBase. - [Read more PROSITE]
Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila. - [Read more Drosophila DNase I footprint database]
TraFaC (Transcription Factor Binding Site Comparison) is a tool that identifes regulatory regions using a comparative sequence analysis approach. - [Read more TraFaC]
Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high sil - [Read more DEQOR]
This resource includes siSearch, AOSearch, and a siRNAdb which provides a platform for mining an siRNA database, and searching for non-specific matches to your siRNA (small interfering RNAs). - [Read more siRNAdb]
Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of the a potential siRNA. - [Read more siRNA Selection Server]
