TFBS 0.7.1 – Perl modules for Transcription Factor Binding Site Detection and Analysis

TFBS 0.7.1

:: DESCRIPTION

TFBS is a set of integrated, object-oriented Perl modules for transcription factor binding site detection and analysis. It implements objects representing specificity profile matrices, binding sites and sets thereof, pattern generators, and pattern database interfaces.

::DEVELOPER

Computational Regulatory Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Perl
bioperl
PDL

:: DOWNLOAD

TFBS

:: MORE INFORMATION

Citation:

Lenhard B., Wasserman W.W. (2002)
TFBS: Computational framework for transcription factor binding site analysis.
Bioinformatics 18:1135-1136

TFBSTools 1.30.0 – Transcription Factor Binding Site (TFBS) Analysis

TFBSTools 1.30.0

:: DESCRIPTION

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites and transcription factor profile matrices.

::DEVELOPER

Computational Regulatory Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R/BioConductor

:: DOWNLOAD

TFBSTools

:: MORE INFORMATION

Citation

TFBSTools: an R/Bioconductor package for transcription factor binding site analysis.
Tan G, Lenhard B.
Bioinformatics. 2016 Jan 21. pii: btw024.

PlantTFcat – Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool

PlantTFcat

:: DESCRIPTION

PlantTFcat is a high-performance web-based plant transcription factor and transcriptional regulator categorization and analysis tool, designed to identify and categorize TFs and TRs in genome-scale protein or nucleic acid sequences.

::DEVELOPER

The Zhao Bioinformatics Laboratory

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Nov 12;14:321. doi: 10.1186/1471-2105-14-321.
PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool.
Dai X, Sinharoy S, Udvardi M, Zhao PX.

DBChIP 1.36.0 – Differential Binding of Transcription Factor with ChIP-seq

DBChIP 1.36.0

:: DESCRIPTION

DBChIP detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples.

::DEVELOPER

Kun Liang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R
BioCOnductor

:: DOWNLOAD

DBChIP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 1;28(1):121-2. doi: 10.1093/bioinformatics/btr605. Epub 2011 Nov 3.
Detecting differential binding of transcription factors with ChIP-seq.
Liang K1, Keles S.

RamseyHAc 2010 – Prediction of Mammalian Transcription Factor Binding Sites

RamseyHAc 2010

:: DESCRIPTION

RamseyHAc (Histone acetylation) is a package of MATLAB M-files and data files is provided. The data files contain the feature tracks used for predicting TF binding sites, and the “ground truth” binding location data used to train the prediction model (both in MATLAB “.mat” file format). Also included is the file “GenomeRegions.bed” (in UCSC BED format) which describes the genome regions analyzed in this study. The M-files are the functions used to predict transcription factor binding, train the prediction model, and test the prediction model in a cross-validation framework.

::DEVELOPER

MAGNET project

:: REQUIREMENTS

Windows/Linux/MacOsX
MatLab

RamseyHAc

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 1;26(17):2071-5. doi: 10.1093/bioinformatics/btq405. Epub 2010 Jul 27.
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.
Ramsey SA1, Knijnenburg TA, Kennedy KA, Zak DE, Gilchrist M, Gold ES, Johnson CD, Lampano AE, Litvak V, Navarro G, Stolyar T, Aderem A, Shmulevich I.

ProbTF – Transcription Factor Binding Prediction from multiple data sources

ProbTF

:: DESCRIPTION

ProbTF provides a flexible and principled probabilistic framework to predict transcription factor binding from multiple data sources. ProbTF uses the standard position specific frequency matrix (PSFM) and the d:th order Markovian background models as its building blocks (this choice is arbitrary though, and similar methods can be implemented using other models as well). In addition, ProbTF can incorporate basically any genome-level information (i.e., information at the level of individual nucleotides) in a probabilistic manner to estimate binding probabilities.

::DEVELOPER

Prof. (pro term) Harri Lähdesmäki, D.Sc. (Tech)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX / Windows
Matlab

:: DOWNLOAD

ProbTF

:: MORE INFORMATION

Citation:

Harri Lähdesmäki, Alistair G. Rust and Ilya Shmulevich,
Probabilistic inference of transcription factor binding from multiple data sources,
PLoS ONE, Vol. 3, No. 3, e1820, 2008.

MICSA – Identification of Transcription Factor binding sites in ChIP-Seq data

MICSA

:: DESCRIPTION

MICSA (Motif Identification for ChIP-Seq Analysis) is package for the identification of transcription factor binding sites in ChIP-Seq data

::DEVELOPER

Boeva lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

MICSA

:: MORE INFORMATION

Citation:

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.
Boeva V, Surdez D, Guillon N, Tirode F, Fejes AP, Delattre O, Barillot E.
Nucleic Acids Res. 2010 Jun;38(11):e126. Epub 2010 Apr 7.

motifStack 1.34.0 – Visualization of Motif Alignment and the analysis of Transcription Factor Binding site Evolution

motifStack 1.34.0

:: DESCRIPTION

motifStack is a package for the visualization of the alignment of motifs as a phylogenetic tree in different layout types. This tool facilitates the analysis of binding site diversity and conservation within families of TFs and the evolution of TFs among different species. motifStack can align DNA motifs; generate motif signatures for closely related motifs; and plot aligned motifs as a stack, a linear or a radial tree, or a word cloud of sequence logos. Different parameter settings can be used to generate diverse types of plots with color schema highlighting important data features.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
BioConductor
R package

:: DOWNLOAD

motifStack

:: MORE INFORMATION

Citation:

Ou J, Wolfe SA, Brodsky MH, Zhu LJ.
visualization of motif alignment and the analysis of transcription factor binding site evolution for the analysis of transcription factor binding site evolution.
Nat Methods. 2018 Jan 3;15(1):8-9. doi: 10.1038/nmeth.4555. PMID: 29298290.

TFBS Scanner – Scanning for Transcription Factor Binding Sites

TFBS Scanner

:: DESCRIPTION

TFBS Scanner provides command line software toolsets for two useful types of TFBS (Transcription Factor Binding Site) Scanning using Positional Weight Matrices (PWMs):

The Scanner Toolset
Scanning with a fixed background model (can be toggled to 0th order or 1st order Markov, currently set as 1st order), with PWM-specific thresholds generated using this same background

The SpeakerScan Toolset
Scanning with a local background correction, outputs log-likelihood scores which can then be post-processed as desired

::DEVELOPER

Megraw Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Java

:: DOWNLOAD

TFBS Scanner

:: MORE INFORMATION

Citation

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M. (2014).
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.
Plant Cell, 26:2746-60.

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. (2009).
A transcription factor affinity based code for mammalian transcription initiation.
Genome Research, 19:644-56.

JASPAR 2020 – Transcription Factor Binding Profile Database

JASPAR 2020

:: DESCRIPTION

JASPAR is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species.

::DEVELOPER

The Wasserman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/MacOsX/Linux
R package/BioConductor/BioPython

:: DOWNLOAD

JASPAR for BioConductor

:: MORE INFORMATION

Citation

Fornes O, Castro-Mondragon JA, Khan A, et al.
JASPAR 2020: update of the open-access database of transcription factor binding profiles.
Nucleic Acids Res. 2019; doi: 10.1093/nar/gkz1001

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, Lim J, Shyr C, Tan G, Zhou M, Lenhard B, Sandelin A, Wasserman WW.
Nucleic Acids Res. 2013 Nov 4.