68
- Create a protomap.params fi le. An example of a protomap.params
fi le is shown in Fig. 3. The protomap.params fi le tells the scripts
how many samples there are, where they are, and in what order
they should be organized. You can download a sample protomap.
params fi le at http://www.scripps.edu/chemphys/cravatt/
protomap. Place it in the folder containing the scripts ( coverage.
pl , protomap.pl , and peptographer.pl ). Then, modify the params
fi le for your own PROTOMAP datasets using a text editor. The
fi rst section of the protomap.params fi le, under the ######
Options ###### header, contains a set of parameters that you
should modify depending on your experiment. Be sure that the
n and numbands parameters correctly specify the number of
replicates and bands, respectively. The next two sections (####
Control bands #### and #### Experimental bands #####)
designate the locations of all of the folders containing your data
from each gel band. There should be the same number of
folders in each section, and each folder should contain
DTAselect.html and DTAselect-fi lter.txt fi les from step 3. Other
fi les in those folders will be ignored. - Run the scripts:
(a) Open a command prompt and navigate to the folder that
contains your scripts, data, and params fi le. Type coverage.
pl and press.
(b) When coverage.pl has fi nished, type protomap.pl and press. It may take some time to run, depending on the
complexity of your data and the speed of your CPU.
(c) When protomap.pl has fi nished, an output fi le called alldata.
pmap is created. It is recommended that you rename this fi le
with a more descriptive fi lename (but keep the .pmap
extension).
Fig. 3 The contents of a typical protomap.params fi le. Parameters specifying the location of the FASTA data-
base and several optional switches for controlling the behavior of the script are specifi ed in the “Options”
section. Below this section are two sections that specify the relative paths of the control and experimental
sections, respectively
Melissa M. Dix et al.http://www.ebook3000.com