The following services were developed in our lab and are available for use:
flyhd - Predicts homeodomain specificity
Colorfy - Color-codes CLUSTAL alignment outputs based on individual column percentage makeup
APACE - Automated Protein Annotation by Coordinate Evolution
GreenGenie2 - Tool for predicting genes in Chlamydomonas reinhardtii
Consensus Server - Web interface for finding DNA and protein patterns
Procom Server - Compare multiple eukaryotic proteomes
Databases and Data files
The following were developed in our lab and are available for use:
HTH Motif Discovery - Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes.
HT_Selex Data - Sequence data for round 0 and round 1 of zif268 Selex.
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 - 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.
TF-BEMs - Transcription Factor Binding Energy Models of Mono-Nucleotides and Di-Nucleotides.
The following programs were developed in our lab and are available for download:
BEEML - Binding Energy Estimation by Maximum Likelihood
StructRED - Structural Cis-Regulatory Element Detector
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 - (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
GRaMS - Growth Rate Modeling of Specificity software
QPLOMA - Quadratic programming method for motif determination with comparison programs
Magma - Multiple alignments of genomic multiple alignments
C elegans PhyloNet - motifs and sites
TF-BEMs - Score Calculation (BEMSER) and Sequence Logo development (EnergyLogo) based upon Binding Energy Models.