There is a graphical way of checking for transmembrane regions. The program is called pepplot and requires that you set the graphics device name prior to running the program. This is done with setplot.

setplot guide

With the graphics device set, run the pepplot program.

pepplot guide

What you are looking for in the graphical output are regions about 20 residues long that are phobic in nature. Phobic areas would be on the upper part of the displayed plot.

composite output

With this information in hand, it is time to visit the transmembrane prediction sites on the web and see what sort of answers they can provide. In the socrates window, enter the command given below to have your data available to paste into the data entry windows of these sites.

cat *.tfa<rtn>

Since the PHDhtm site only returns email responses, visit that site first in hopes that you might get a reply before the class ends.

Most of these sites produce an html page containing your prediction. To keep track of your results, create a file on socrates with pico and paste into it the relevant information as it is generated.

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