Help info for using PerfectMatch program:

         New! The parameter files had been updated to the latest version from Affymetrix , please download and using the new files for perfectmatch program.

Download the new update for PerfectMatch package (updated on 04-04-2005; v2.3.3). Then unzip the files and run the setup program. You will also need a set of sequence and parameter files to run the program. Please choose the array type and download the files. After download these files, you need to unzip them and use it in the PerfectMatch program.

Human Genome U133A             Human Genome U133A2.0               Human Genome U133 Plus 2.0                                      

Human Genome U95Av2           Murine Genome U74Av2                   Mouse Genome 430 2.0                    Mouse Genome 430A 2.0                

Download : the PerfectMatch Program Manual in PDF format.

Download the PDNN paper: Note that the PDF file on this website is slightly different from the one published on Nature Biotechnology journal that contained a few mistakes in the figure legends.

     Download Probe Binding Energy Calculator here. This program can compute probe binding energy for any given probe sequences using PDNN parameters.  This program is created for evaluating probe performance to assist probe design.

    Contact: If you have any question concerning PerfectMatch Program, please email or