Services

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.

Software

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.