Paper Figures
PeakFinder Program

The PeakFinder program was developed to find cohesin binding sites represented by the peaks in yeast chromatin immunoprecipitation (ChIP) microarray data, but can be applied to plot any measurement against a parameter such as genome coordinate, to interactively analyze the measurement plot, and to annotate the peaks on the basis of local properties of the curve.

Software Requirements.  PeakFinder was developed and tested under Windows 2000 (but should work under Windows 98 or later).  PeakFinder works best with a high-color or true-color display monitor, and requires a resolution of 1280-by-1024 or larger.  PeakFinder provides sample data to exercise the various program options.

Installation.  The Installshield installation program installs PeakFinder in its own C:\PeakFinder directory.  Start the program from the desktop icon:

Or, use: Start | Programs | PeakFinder.

In addition to the program, the C:\PeakFinder directory contains sample Excel spreadsheets, Coordinates.xls and Ratios.xls.  The C:\PeakFinder\Yeast directory has yeast (S. cerevsiae) nucleotide files in FASTA format, one for each chromosome.  The C:\PeakFinder\Documenation directory contains the Quick Start Guide and User's Guide in PDF format.


Peak finder is written in Delphi, runs on a Windows platform and is distributed under the GNU General Public License.  The source code is available by contacting the author.