FLRTFM

Description

FLRTFM (“Firth Logistic Regression Transcription Factor Models”) is a free script written by Ji-Hyun Lim. FLRTFM uses combined sequence and histone modification data to predict transcription factor binding sites.

Currently, FLRTFM implements a combined-evidence model to predict p53 binding sites in the human genome. Users may wish to develop new models and modify FLRTFM to search for other transcription factor binding sites.

Download

To obtain FLRTFM Version 1.0 for Linux and Mac OS X, download the supplementary data for the following paper:

Lim, J.-H., Iggo, R.D. and Barker, D. 2013. Models incorporating chromatin modification data identify functionally important p53 binding sites. Nucleic Acids Research, 41, 5582-5593.

Within the supplementary data, the file “nar-00606-n-2013-File020.zip” unzips to give a directory named “script”. This contains FLRTFM.

Citing FLRTFM

Please cite this paper if you use FLRTFM:

Lim, J.-H., Iggo, R.D. and Barker, D. 2013. Models incorporating chromatin modification data identify functionally important p53 binding sites. Nucleic Acids Research, 41, 5582-5593.

FLRTFM uses other software and resources, as outlined in a comment at the start of the file “predict_a_given_site_for_p53_binding_using_combined_model.pl”. Please cite these as well as the above paper.

Support

Please send questions and bug reports to:

Funding

We are grateful to the Biotechnology and Biological Sciences Research Council for financial support.