Beginning Perl for Bioinformatics

Chapter 2. Getting Started with Perl

Perl is a popular programming language that’s extensively used in areas such as bioinformatics and web programming. Perl has become popular with biologists because it’s so well-suited to several bioinformatics tasks.

Perl is also an application, just like any other application you might install on your computer. It is available (at no cost) and runs on all the operating systems found in the average biology lab (Unix and Linux, Macintosh, Windows, VMS, and more).^[1] The Perl application on your computer takes a Perl language program (such as one of the programs you will write in this book), translates it into instructions the computer can understand, and runs (or “executes”) it.

So, the word Perl refers both to the language in which you will write programs and to the application on your computer that runs those programs. You can always tell from context which meaning is being used.

Every computer language such as Perl needs to have a translator application (called an interpreter or compiler) that can turn programs into instructions the computer can actually run. So the Perl application is often referred to as the Perl interpreter, and it includes a Perl compiler as well. You will often see Perl programs referred to as Perl scripts or Perl code. The terms program, application, script, and executable are somewhat interchangeable. I refer to them as “programs” in this book.

A Low and Long Learning Curve

A nice thing about Perl is that you can learn ...