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Several individual tools for transcription factor binding site analysis exist. TFBSTools is a suite incorporating a range of tools in a single package, including:

  • Handling TFBS profile matrices
    - Converts between position frequency matrix (PFM), position weight matrix (PWM) and information content matrix (ICM)
    Compares pairs of PFMs, or a PFM with IUPAC strings
    - Manipulatestranscription factor flexible model (TFFM) profiles 

  • Scanning sequences and alignments including whole genomes for TBFSs
    - Screens potential TFBSs present in a DNA sequence (searchSeq), or conserved in a pairwise alignment
    Phylogenetic footprinting supported (when a pairwise alignment is available)

  • Querying and manipulating the JASPAR database

  • Wrapper functions for de novo motif discovery software

The functionality of the package can be easily extended to include advanced statistical analysis, data visualization and data integration

 

TFBSTools can be downloaded from:

http://bioconductor.org/packages/release/bioc/html/TFBSTools.html

 

More information can be found in the following paper:

Tan and Lenhard (2015) TFBSTools: an R/bioconductor package for transcription factor binding site analysis, Bioinformatics 32(10), 1555–1556

 

Internal case number 8156

TFBSTools

Extensive suite of tools for transcription factor binding site analysis

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