USING PERL TO FACILITATE BIOLOGICAL ANALYSIS

The Cold Spring Harbor Laboratory Cold Spring Harbor, New York 

It should be immediately apparent that there are some problems with this approach. If there are more than just a few genes of interest to analyze, the job quickly becomes rather tedious, if not overly time consuming. Worse yet, the next time that new RNAi results are released, the whole process will need to be repeated, determining which RNAi entries are new. The step involving loading WormPep into a word processor might not even be tenable due to the sheer size of the database, well over 10 megabases. 

Perl interpreters are available for the Macintosh, Windows, and UNIX operating systems and more often than not is made available as freeware. A number of download sites are listed at the end of this chapter. Because Perl program files are usually compressed to speed downloads, Macintosh users will need to use a utility like UnStuffIt to uncompress the package, whereas Windows users will need WinZip or PKZip. Perl should come as part of the standard software installation on most UNIX-based machines. Typing perl -v at the UNIX prompt will indicate whether the program is indeed installed and, if so, the version number that is available on that machine. 

The process of writing and rimning a Perl script is similar on Windows and UNIX systems but slightly different for Macintosh users. The basic steps are described below. 

On a Windows or UNIX system, create a text-only file containing the following lines  

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USING PERL TO FACILITATE BIOLOG 1CAL ANALYSIS... 

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