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:

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.