Transcription Factors

BARTweb

BARTweb (Binding Analysis for Regulation of Transcription) - This web server is to perform BART, a bioinformatics tool for predicting functional factors (including transcription factors and chromatin regulators) that bind at cis-regulatory regions to regulate gene expression in human or mouse, taking a query gene list or a ChIP-seq dataset as input.
(Reference: Ma W et al. (2021) NAR Genom Bioinform 3(2):lqab022).

Cistrome-GO

Cistrome-GO - previously, this group developed a widely used method, BETA, to integrate TF ChIP-seq peaks with differential gene expression (DGE) data to infer direct target genes. Here, we provide Cistrome-GO, a website implementation of this method with enhanced features to conduct ontology analyses of gene regulation by TFs in human and mouse. Cistrome-GO has two working modes: solo mode for ChIP-seq peak analysis; and ensemble mode, which integrates ChIP-seq peaks with DGE data.
(Reference: Li S et al. (2019) Nucleic Acids Res 47(W1): W206-W211).

Tfsitescan

Tfsitescan (Institute for Transcriptional Informatics, Pittsburgh, U.S.A.) - This tool is intended for promoter sequence analysis and works best with sequences of ~500 nt.

PlnTFDB

PlnTFDB - Plant Transcriptional Factor Database - allows BLAST searching
(Reference: P. Pérez-Rodríguez et al. 2009 Nucl. Acids Res. 38: D822-D872) or here for related site.

DBD

DBD - Transcription factor prediction database (Gesellschaft für Biotechnologische Forschung mbH (GBF), Braunschweig, Germany)
(Reference: D. Wilson et al. 2010. Nucl. Acids Res. 36: D88-D92)

rVista

rVista (Comparative Genomics Center, Lawrence Livermore National Laboratory, U.S.A.) - High-throughput discovery of functional regulatory elements in sequence alignments. Excluding up to 95% false positive transcription factor binding sites predictions while maintaining high sensitivity of the search.

TFmiR

TFmiR - for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis.
(Reference: Hamed, M. et al. 2015. Nucl. Acids Res.).

ISMARA

ISMARA (Integrated System for Motif Activity Response Analysis) - is an online tool that models genome-wide expression or ChIP-seq data, in terms of computationally predicted regulatory sites for transcription factors (TFs) and micro-RNAs (miRNAs). The only input required for running ISMARA is either expression data (microarray CEL files or RNA-seq FASTQ and BED/BAM/SAM alignment files), or ChIP-seq data (FASTQ and BED/BAM/SAM alignment files), from a set of biological samples.
(Reference: Balwierz PJ et al. (2014) Genome Res 24(5): 869-884). Requires registration.

TRANSFAC

TRANSFAC - offers academic and non-profit organizations free access to TRANSFAC® non-professional 2005 version with much reduced functionality and content compared to our professional database. Provides access to programs including Match which is a weight matrix-based program for predicting transcription factor binding sites (TFBS) in DNA sequences. It uses a library of positional weight matrices from TRANSFAC® Public 6.0; and, P-Match - a program for predicting transcription factor binding sites (TFBS) in DNA sequences that combines pattern matching and weight matrix approaches. It uses a library of positional weight matrices from TRANSFAC® Public 6.0 along with the site alignments associated with these matrices.

PRODORIC

PRODORIC - is the most comprehensive database about gene regulation and gene expression in prokaryotes founded in 2003. It includes a manually curated and unique collection of transcription factor binding sites. A variety of bioinformatics tools for the prediction, analysis and visualization of regulons and gene regulatory networks is available.
(Reference: Dudek, CA & Jahn, D. (2022). Nucleic acids research, 50 (D1): D295-D302). Logo for DnaA-binding site:

LogoMotif

LogoMotif - is an up-to-date comprehensive database on gene regulation in Actinobacteria. It contains curated experimentally-validated transcription factor binding site (TFBS) profiles and preconstructed position frequency matrices (PFMs) and position weight matrices (PWMs). The matrices are pre-applied to several model organisms to detect TFBS locations and construct gene regulatory networks.
(Reference: Augustijn HE et l. (2023) J. Molec Biol 436(17): 168558)

JASPAR CORE

JASPAR CORE - (check tools) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups.
(Reference: Fornes O et al. (2019) Nucleic Acids Res. 48(D1): D87-D92).

ConTra v3

ConTra v3 - is a tool to identify transcription factor binding sites across species. ConTra v3 can analyze promoter regions, 5?-UTRs, 3?-UTRs and introns or any other genomic region of interest. Thousands of position weight matrices are available to choose from for detecting specific binding sites.
(Reference: Kreft L et al. (2017) Nucleic Acids Res; 45(W1): W490-W494).

RegRNA 3.0

RegRNA 3.0 - is a sophisticated meta-workflow that integrates 26 computational tools and 28 databases for annotation, enabling one-step and customizable RNA motif predictions. RegRNA streamlines multi-step analysis and enhances result interpretation with interactive visualizations and comprehensive reporting tools. When provided with an RNA sequence, RegRNA 3.0 generates predictions for RNA functional motifs, RNA interaction motifs, and comprehensive RNA annotations. Specifically, RNA functional motifs include core promoter elements, RNA decay, G-quadruplex, and 14 previous types. RNA interaction motifs include newly added RNA-ligand interactions and RNA-binding protein predictions, along with three previous types. RNA annotation includes RNA family classification, blood exosomes RNA, subcellular localizations, A-to-I editing events, modifications, and 3D structures, along with four previously supported features.
(Reference: Huang Y et al. 2025. Nucleic Acids Research 53(W1): W485 - W495).

Updated: February, 2026