This page provides a link to download the training/validation dataset and the MATLAB software that was developed for the Ramsey, Knijnenburg et al. study in which histone acetylation ChIP-Seq data were used to improve motif scanning-based prediction of transcription factor binding sites. Specifically, a package "RamseyHAc2010" 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.
Please note: The M-files in this package were developed and tested in the MATLAB envirionment, release R2009b, in two different installations: 64-bit Intel Linux and 64-bit Intel Mac OSX. The M-files have not been tested in other MATLAB installations (such as MATLAB installations on Windows, or 32-bit MATLAB installations). The following list summarizes the software requirements for using this package:
RamseyHAc2010.tar.gz (65 MB)
A detailed README.txt file is included with this software package that gives step-by-step instructions for how to install and use the software package, as well as detailed function-level documentation on all of the M-files included in the package.
The software is provided under the BSD license:
Copyright (c) 2010, Institute for Systems Biology
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
- Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
- Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
- Neither the name of the Institute for Systems Biology nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Last modified: 2010/06/30