Gene Regulation

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]

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]

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]

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]

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]

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]

Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles. - [Read more Consite]

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]

This website contains microarray analysis software (Argus and Z-pool), an Endothelial Cell Expression Database, and other resources related to Vascular Endothelium research. See the PubMed abstracts for more information. - [Read more Defining Transcriptional Programs in Vascular Endothelium]

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]

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]

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]

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]

Access to databases, programs and papers related to gene regulation. - [Read more Gene Regulation]

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]

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]

Search for potential transcription factor binding sites in your own sequences using TRANSFAC matrices; free for non-commercial use. - [Read more MatInspector]

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]

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]

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]

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]

Compares two DNA sequences allowing for inversions and translocations, ideal for promoters. - [Read more PromoterWise]

Database of protein families and domains defined from SwissProt database; consider also checking specific motif databases such as PhosphoBase. - [Read more PROSITE]

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]

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]

RiceTFDB(Rice Transcription Factor DataBase) is a database of sequences and alignments for transcription factors in Rice. - [Read more RiceTFDB]

Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis. - [Read more rVISTA]

Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features. - [Read more Sfold]

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]

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]