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Transcription factor binding site (TFBS) detection software tools | Genome annotation

Prediction of transcription factor binding sites (TFBSs) is crucial for promoter modeling and network inference. Quality of the predictions is spoiled by numerous false positives, which persist as the main problem for all presently available TFBS…
TFBS
Desktop

TFBS Transcription Factor Binding Site analysis

Permits transcription factor binding site detection and analysis. TFBS is a…

Permits transcription factor binding site detection and analysis. TFBS is a package that provides a set of integrated, object-oriented Perl modules. It integrates generation, manipulation, storage…

CMA
Web

CMA Composite Module Analyst

Identifies promoter-enhancer models based on the composition of transcription…

Identifies promoter-enhancer models based on the composition of transcription factor binding sites (TFBS) and their pairs. CMA uses an approach for defining a promoter model based on composition of…

ConTra
Web

ConTra conserved TFBSs

VIB Bioinformatics Core, Zwijnaarde-Ghent, Belgium; VIB-UGent Center for…

VIB Bioinformatics Core, Zwijnaarde-Ghent, Belgium; VIB-UGent Center for Inflammation Research, Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University,…

INSECT
Web

INSECT IN-silico SEarch for Co-occurring Transcription factors

Allows to analyze genomic sequence data for in silico cis-regulatory modules…

Allows to analyze genomic sequence data for in silico cis-regulatory modules (CRMs) prediction and analysis. INSECT is a web server which allows a complete and flexible analysis of the predicted…

TFImpute
Desktop

TFImpute

Implements a method for accurately predicting cell-specific transcription…

Implements a method for accurately predicting cell-specific transcription factor (TF) binding for TF-cell line combinations based on only a small fraction (4%) of the combinations using available…

PROMO
Web

PROMO

A virtual laboratory for the study of transcription factor binding sites (TFBS)…

A virtual laboratory for the study of transcription factor binding sites (TFBS) in DNA sequences. PROMO is a program for the prediction of TFBS in a single sequence or in a group of related…

MatInspector
Desktop

MatInspector

Identifies transcription factor binding sites (TFBS) in nucleotide sequences…

Identifies transcription factor binding sites (TFBS) in nucleotide sequences using a large library of weight matrices. MatInspector produces concise results avoiding redundant and false-positive…

PhysBinder
Web

PhysBinder

Predicts transcription factor binding sites (TFBS). PhysBinder algorithm makes…

Predicts transcription factor binding sites (TFBS). PhysBinder algorithm makes use of both direct (the sequence) and indirect readout features (biophysical properties such as the bendability of the…

ORCAtk
Web
Desktop

ORCAtk ORCA toolkit

A software package developed in support of diverse regulatory sequence analysis…

A software package developed in support of diverse regulatory sequence analysis projects associated to the PAZAR database of gene regulatory information. ORCAtk is a system for finding putative…

BPAC
Web
Desktop

BPAC Binding Prediction from ACcessibility data

Allows to predict transcription factor (TF) binding events, using available TF…

Allows to predict transcription factor (TF) binding events, using available TF ChIP-Seq data as a gold standard. BPAC is a supervised classification approach which selects the features from sequence…

RcisTarget
Desktop

RcisTarget

Identifies enriched transcription factor (TF) binding motifs and candidates TF…

Identifies enriched transcription factor (TF) binding motifs and candidates TF for a gene list. RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the…

PREDetector
Web

PREDetector

Identifies putative transcription factor-binding sites (TFBS) in bacterial…

Identifies putative transcription factor-binding sites (TFBS) in bacterial genomes. PREDetector allows users to freely fix the DNA-motif screening parameters, and provides a statistical means to…

MATCH
Desktop

MATCH

Searches putative transcription factor binding sites in DNA sequences. Match is…

Searches putative transcription factor binding sites in DNA sequences. Match is closely interconnected and distributed with the TRANSFAC database. It uses a library of mononucleotide weight matrices…

ASAP
Web
Desktop

ASAP

Can be used for fast searching with position weight matrices that include…

Can be used for fast searching with position weight matrices that include several standard methods for assessing over-representation. ASAP is significantly faster than more naïve scanning algorithms…

ProbTF
Web

ProbTF Probabilistic Inference of Transcription Factor Binding

Predicts transcription factor binding using experimentally verified Position…

Predicts transcription factor binding using experimentally verified Position Weight Matrices (PWMs). ProbTF provides a probabilistic framework which has three important features. First, ProbTF is…

SparScape
Desktop

SparScape

Identifies DNA binding factors (DBFs) active in the considered regions and…

Identifies DNA binding factors (DBFs) active in the considered regions and predicting a joint probabilistic binding landscape. SparScape is able to select a small subset of DBFs with enriched binding…

PromoterSweep
Web

PromoterSweep

An automated bioinformatics pipeline to analyse promoter sequences and predict…

An automated bioinformatics pipeline to analyse promoter sequences and predict transcription factor binding sites. PromoterSweep uses a combination of different tools: sequence comparison to promoter…

SiTaR
Web

SiTaR Site Tracking and Recognition

A straightforward method for nucleotide composition-based detection of…

A straightforward method for nucleotide composition-based detection of non-random matching motifs applied to prediction of transcription factor binding sites (TFBSs). One of the evident advantages of…

TFBIND
Web

TFBIND Transcription Factor BINDing site

Searches transcription factor binding sites (TFBS). TFBIND uses weight matrix…

Searches transcription factor binding sites (TFBS). TFBIND uses weight matrix in TRANSFAC R.3.4 database for detecting its preferred binding region in promoters. TFBIND includes the method of…

PIPES
Desktop

PIPES Probabilistic Integration of PBM Epigenetics and Sequence data

Predicts tissue-specific transcription factor (TF) binding. PIPES integrates in…

Predicts tissue-specific transcription factor (TF) binding. PIPES integrates in vitro protein binding microarrays (PBMs), sequence conservation and tissue-specific epigenetic information. PIPES is…

SCintuit
Desktop

SCintuit

A scoring method for measuring sequence-motif affinity based on intuitionistic…

A scoring method for measuring sequence-motif affinity based on intuitionistic fuzzy sets (IFS) theory. SCintuit is designed to prevent overestimation of less conserved positions of transcription…

Patch
Web

Patch

Predicts transcription factor binding sites (TFBS) in DNA sequences. Patch uses…

Predicts transcription factor binding sites (TFBS) in DNA sequences. Patch uses the set of binding sites from TRANSFAC.

tfscan
Desktop

tfscan

Identifies transcription factor binding sites (TFBS) in DNA sequences. tfscan…

Identifies transcription factor binding sites (TFBS) in DNA sequences. tfscan scans one or more DNA sequences for TFBS from the TRANSFAC database. The taxonomic group can be specified. An output file…

VOMBAT
Web

VOMBAT

Improves the recognition and the prediction of binding sites for transcription…

Improves the recognition and the prediction of binding sites for transcription factors. VOMBAT allows users to apply different combinations of markov models and bayesian trees to DNA sequences. Tasks…

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