Perl makes it easy to start other programs and collect their output, all from within your Perl program. This is an extremely useful capability; for most programs, Perl makes it fairly simple to accomplish.
You may need to run some particular program many times, for instance over every file in PDB to extract secondary structure information. The program itself may not have a way to tell it "run yourself over all these files." Also, the output of the program may have all sorts of extraneous information. What you need is a much simpler report that just presents the information that interests you—perhaps in a format that could then be input to another program! With Perl you can write a program to do exactly this.
An important kind of program to automate is a web site that provides some useful program or data online. Using the appropriate Perl modules, you can connect to the web site, send it your input, collect the output, and then parse and reformat as you wish. It's actually not hard to do! O'Reilly's Perl Cookbook, a companion volume to Programming Perl, is an excellent source of short programs and helpful descriptions to get you started.
Perl is a great way to automate other programs. The next section shows an example of a Perl program that starts another program and collects, parses, reformats, and outputs the results. This program will control another program on the same computer. The example will be from a Unix or Linux environment; consult your Perl ...