Scanning for Transcription Factor Binding Sites
Note: This tool and website are now dated, please consider using a newer extended version of these tools available as the TFBS Scanner Suite.
This website provides command line software toolsets for two useful types of TFBS (Transcription Factor Binding Site) Scanning using Positional Weight Matrices (PWMs):
- The Scanner Toolset (Scanner.tgz):
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 (SpeakerScan.tgz):
Scanning with a local background correction, outputs log-likelihood scores which can then be post-processed as desired
Description
Each toolset directory provides a working example intended to run out-of-the-box with provided shell script (Scanner/Scan/scan.sh and SpeakerScan/run.sh) on any unix or linux system. Simply download the intended toolset above (by clicking Scanner.tgz or SpeakerScan.tgz above), and unpack the archive (e.g. tar -xzf Scanner.tgz).
Core source code is written in Java (GNU public license), with helper scripts in Perl and Bash, by Molly Megraw (Scanner Toolset threshold program was converted to C++ for speed, courtesy of Bill Majoros).
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 additional related tools and publications, please visit the Uwe Ohler 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:
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.
About this website:
This material is based upon work supported by the National Science Foundation under Grant No. 0805648.
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 Science Foundation (NSF).
