Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles. - [Read more Consite]
Aligns Nucleic Acid Conserved Elements; uses pattern recognition to find elements conserved in a set of DNA sequences; free for non-commercial use with license agreement. - [Read more AlignACE]
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 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]
Analyzes a set of DNA or protein sequences for similarities among them and produces a description (motif) for each pattern it discovers. - [Read more MEME]
Search for potential transcription factor binding sites in your own sequences using TRANSFAC matrices; free for non-commercial use. - [Read more MatInspector]
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]
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]
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. - [Read more MotifViz]
This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3. - [Read more eBioinformatics]
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]
MaskerAid is an enhancement to RepeatMasker which can effect about a 30-fold increase in the speed of RepeatMasker while maintaining sensitivity. - [Read more MaskerAid]
BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl). - [Read more BioMart]
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]
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]
Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis. - [Read more rVISTA]
IslandPath aids genomic island detection in prokaryotic genome seqeunces, using features such as dinucleotide bias, G+C, location of tRNA genes, annotations of mobility genes, etc. Genomic islands are defined here as genomic regions of potential horizonta - [Read more IslandPath]
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]
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 aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site. - [Read more PromoSer]
Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use. - [Read more TRANSFAC]
Screens a DNA sequence against a library of repetitive elements; returns a masked query sequence and a table annotating the masked regions. - [Read more RepeatMasker]
