Here is an example to use regionDetect.exe in the directory UI.

At the very beginning, the users should put the files genetic_map_chr1_b36.txt, hapmap3_r2_b36_fwd.consensus.qc.poly.chr1_jpt+chb.unr.phased, pedigree.ped, and children.ped into the same directory as regionDetect.exe(here UI). The pedigree we use is the one given in the home page.

Start to run the program by double-clicking the regionDetect.exe file, a message box will pop up.

After a while, the main frame will appear. The menubar provides the operation options, the content panel shows the whole chromosome represented with a blue line, and the string at the right side of the status bar indicates the index of the SNP site your mouse pointer ponits to.

If you right-click one specific site, its real position on the chromosome and genetic map will be shown on the content panel.

click operation in the menubar and select " start to compute ". A dialog box will pop up for you to set values of the parameters.

1.people No. indicates the number of individuals in the file pedigree.ped.

2.input individuals No. indicates the number of closely related individuals in the file children.ped.

3.diseased position indicates the assumed mutation position causing the disease.

4.delta indicates the maximmum allowed distance between the center haplotype and some haplotype in the database(for details see the paper.

5.step indicates the length of the chromosome segments

As shown in the picture, if you are ready for all the parameters, click the button OK to start.

After about 10 minutes, the program will output the results in two forms.

1. result in the interface. As shown in the below picture: the whole blue line represents the whole chromosome. The red line segments represent the reported linked regions. And the green line segment indicates the real mutation region.

2.linked_region_10f.txt. A typical one is shown in linked_region_10f.txt

Then click merge close segments in the menu list, the result is show below, and the output file is : linked_region_10f_3500.txt

After that click extend2000 to further refine the result as shown in the below figure and linked_region_10f_extend2000.txt

The way to run regionDetect-formal.exe is similar to regionDetect.exe.