Services
The following services were developed in our lab and are available for use
Consensus Server Web interface for finding DNA and protein patterns
Procom Server Compare multiple eukaryotic proteomes
Databases
The following databases were developed in our lab and are available for use
Shewanella oneidensis RNA Database Database of cis-regulatory RNA structural elements in Shewanella oneidensis
Shewanella oneidensis DNA motifs Shewanella oneidensis predicted cis-regulatory DNA motifs
PromoLign Promolign provides graphical presentation for SNPs and transcription factor binding sites in the promoter region of genes in the context of human-mouse orthologous sequence alignment.
Probes for DNA Microarray DNA probe database for DNA Oligo microarray.
EGR SELEX/phage display data set The complete EGR SELEX/phage display data set A collection of some of the published site-specific DNA-protein contacts for Zif268, alias NGFI-A, Egr1, Krox-24, and closely related proteins.
The following is a commercial database available for use by Stormo Lab. Login required.
TRANSFAC Pro version 11.4 A commercial database from Cognia on eukaryotic cis-acting regulatory DNA elements and trans-acting factors. Login required.
Software
The following programs were developed in our lab and are available for download.
RSSVM RSSVM (RNA Sampler + SVM), the Support Vector Machine (SVM) based RNA motif identifier for RNA Sampler generated common RNA structures and alignments.
zifNet For context-depedent DNA recognition code for C2H2 Zinc figner transcription factors
RNASampler A sampling based algorithm for RNA secondary structure prediction.
Probe Select Probe Select.
CRML Web interface for locating muscle-specific regulatory modules in C. elegans sequences.
LOCUS Locus (Length Optimized Characterization of Unknown Spliceforms) evidence-based gene finding algorithm
comRNA A common RNA secondary structure predictor
MatAlign Matrix Aligner
PhyloCon Phylogenetic Consensus, combining phylogenetic data with coregulated genes to identify regulatory motifs
PhyloNet Motif Discovery at Whole Genome Level
Co-Bind Identify target sites for cooperatively binding transcription factors
PromFD Predict promoter regions in DNA sequences
GeneParser Find genes in a genome
Landscape Build gene landscape for intron and exon prediction
Patser Patser find locations of patterns in sequence
Consensus Find DNA and protein patterns
Consensus Server Web-based graphical interface for consensus, wconsensus, & consensus-vio