Software and Datasets

The source code for much of the newer Wasserman Lab software is available on GitHub

Name Description PubMed ID
ASB data set ASB data set contains 10,765 ASB events retrieved from 45 ENCODE ChIP-Seq data sets. 27492288
BiasAway An open-access tool for generating multiple different sequence backgrounds of comparable nucleotide composition relative to a set of input sequences: 24927817
Bioconductor data package for JASPAR Transcription factor binding profile Bioconductor data package 26531826
cis-reg-pred Open-access tool for the segmentation of the human genome. The tool uses a supervised machine learning approach to segment the human genome using experimental data in the same spirit as Segway and ChromHMM.
DNAshapedTFBS Python module allowing for the construction and application of machine learning classifiers combining TFFM/PSSM + DNA shape features for improving the predictions of TFBSs in ChIP-seq data-sets. Highlighted by PMID: 27684185 27546793
IEMBase An expert knowledgebase and diagnosis support tool for inborn errors of metabolism:
IndelImpact Open-access software for the computation of the impact of insertions and deletions on transcription factor binding sites.
JASPAR The 2016 version of the JASPAR database was publicly released on November 2016 and greatly expands the number of transcription factor binding profiles from 2014. Additionally, transcription factor flexible models (TFFMs) have been provided for 130 of the transcription factors. The structural annotation of the TF DNA binding domains (DBDs) has been changed to follow a published hierarchical structural classification and a new web tool has been included to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Finally, A Ruby API module has been created to accompany the existing Perl and Biopython APIs and R/Bioconductor data package:  26531826
JASPAR Biopython module Biopython package to access and use JASPAR binding profiles. 26531826
JASPAR BioRuby gem Ruby gems for parsing, searching, and comparing JASPAR motifs; Based on Bio.motifs module in Biopython. 26531826
MANTA SNV impact on TFBSs 25903198
TFBS perl modules Perl modules for transcription factor binding site detection and analysis 26531826
TFBSTools R/bioconductor package for transcription factor binding site analysis 26794315
TFBS_Visualization An open-access tool for visualizing and assessing transcription factor topological motif enrichment in ChIP-Seq datasets:
TFCat TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature:  19284633
TFFM Transcription Factor Flexible Models (TFFMs) are hidden Markov model (HMM) representations of TFBS motifs. This online tool allows you to generate TFFMs and scan sequences with them: 24039567

Retired Software and Datasets

Name Description PubMed ID
ABC4DE The ABC4DE web-interface allows for the analysis of sets of variants within a region of interest. For a given variant, the tool reports: 1) if it falls within a predicted regulatory region; 2) the predicted role for that region (promoter/enhancer); and 3) if the variant will alter a potential TFBSs.
CAGEd-oPOSSUM The webtool allows for the motif enrichment analysis of CAGE-derived transcription start sites (TSSs): 27334471
DECRES Deep learning for identifying cis-regulatory elements and other applications.
Deep Learning Package in Python Based on The Deep Learning Tutorials and Theano This deep learning package is an extension of the Deep Learning Tutorials (
Gene Characerization Index A bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described: 18213364
MeSHOP Using Medical Subject Heading Overrepresentation Profiles (MeSHOPs), an entity of interest can be robustly summarized, quantitatively identifying associated biomedical terms and suggesting indirect associations: 23017167
MSCAN Algorithm that detects clusters of transcription factor binding sites in genomic sequences: 15215379
NHRscan A computational predictor of nuclear hormone receptor binding sites:  15563547
oPOSSUM3 A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences:  22973536
ORCAtk Transcription factor binding site detection using phylogenetic footprinting (alternative to ConSite):   18971253
PAZAR An open-access system for the collection and dissemination of regulatory sequence annotation: 17916232
TFe An online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes: 22458515
ConSite Transcription factor binding site detection using phylogenetic footprinting. Note that this is an older tool which is hosted remotely. You may also be interested in our ORCAtk tool which is maintained locally and performs similar functionality:  15215389
dbMTN Multiple Tissue Northern Blot Comparison Tool: 18629180
Gene Set Builder A tool for collation, curation and distribution of sets of genes: 16371163
GeneLynx A portal to the human genome. This tool was developed to fulfill a need for easily accessible gene information at a particular point in time. Having fulfilled its purpose, this tool has been retired. Current tools are available to provide similar services. 11731507
GOToolBox Functional Investigation of Gene Datasets: 15575967
JASPAR 2014 The 2014 version of the JASPAR database was publicly released on November 2013 with the incorporation of new and updated transcription factor binding profiles. Beyond the transcription factor binding profiles, we provide the ChIP-seq derived sequences that have been used to construct the profiles. 24194598
NovelFam3000 A bioinformatics tool created to accelerate characterization of gene families sharing uncharacterized protein domains 16533400
oPOSSUM2 v2 (2008) Web-based analysis of over-represented transcription factor binding sites: 17576675
OrthoSeq Alignment of DNA sequences:
PFOND Developed by the Wasserman Laboratory at UBC, PFOND is a web-based service to promote the sharing of information about research, treatment, and resources for rare genetic disorders: 23920006
RAVEN Regulatory analysis of Variation in ENhancers:  18208319
SAGE2Splice A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome:  16683015
Ulysses Protein Interactions Conserved Across Evolution: 16356269