TFBS Scanner Suite

Transcription Factor Binding Site Scanner Suite

This website provides command line software toolsets for TFBS (Transcription Factor Binding Site) Scanning using Positional Weight Matrices (PWMs):

  • The TFBS Scanner Suite:

    A suite of tools that puts all of your scanning needs in one place. The TFBS Scanner Suite consists of one program that has a number of pre-built tools that can be called using a command for each tool:
    • Scan: The main scanning utility which scans transcription factor binding sites using a defined set of user thresholds and PWMs. (Scan Tool Example)
    • Thresholds: A java interface to the 'get-WMM-cutoff' C binary to generate loglikelihood score cutoffs using false positive or false negative rates. 
    • Background: A simple utility to pre-compute the 0th and 1st order Markov background model matrices. 
    • ROEFinder: A utility to generate regions of enrichment for transcription factor binding site matrices that can be used to generate features needed for model building. 
    • GenFeatures: A utility to generate the features needed for building a model.
    • PWMPrint: A utility for normalizing your PWMs. 
    • MakePWMs: A utility for generating PWMs from a list of user sequences. 

    In order to run the tools you will need only two pieces of software:

    1. The TFBS Scanner Suite jar file
    2. The C binary get-WMM-cutoff used by the 'Thresholds' utility for calculating the thresholds. *Note: this file must be in your path for the 'Threshold' utility to work. Currently only a 64-bit linux binary is made available here.

    All the source code files for the scanning suite can be found here.

    Description

  • Core source code is written in Java (GNU public license) by Molly Megraw. Major software additions and packaging as the Scanner Suite were contributed by Jason Cumbie (Megraw Laboratory). The Threshold portion of the program was converted to C++ for speed, courtesy of Bill Majoros (previously of the Ohler Laboratory).

    Related Materials

  • For a straightforward step-by-step explanation of TFBS scanning, please see
    Hatzigeorgiou AG, Megraw M (2010). MicroRNA Promoter Analysis. In Methods in Molecular Biology, 592:149-61.   [Link to Supplementary Material]

    For scanning with either a fixed or local di-nucleotide background model, please see
    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.

    For an application of the tools packaged in the Scanner Suite, please see
    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.

    For additional related tools and publications, please visit the Megraw Laboratory website.

    Citation

  • If any of these tools are used for work which results in a publication, we would appreciate citation of the following article: 
    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.

     

    About this website: 
    This material is based upon work supported by the National Insituties of Health under grant GM097188 to Molly Megraw.
    Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Insitutes of Health (NIH).