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:
BEnDS – Binding Energy Distribution Simulator
BEESEM – Binding Energy
Estimation on SELEX with Expectation Maximization (source code on github)
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.