Why is perl useful for biologists (including bioinformatics people)? You can do a lot of bioinformatics research without programming since there are a lot of existing softwares. But what if you can't find a program which will do exactly what you want? Or you want to do some simple analysis, which can be done with pre-existing, but a complicated program. It is sometime quicker to make the simple analysis program than trying to spend hours learning how to use the pre-existing program, whose features you probably don't need in the future.
More frequently, I encounter situations where there are several steps for the analysis, and the steps are done by different pre-existing programs. Those patient people can sit in front of the computers for hours, and repeat the steps by hand. If you find a mistake in your analysis, you can start over from the beginning by hand. But with perl, you can join the programs and automate the analysis: i.e., create a small program, which will drive the other programs. The analysis is repeatable, and easy to fix problems, or redo similar analysis with many data sets.
Perl is a wondeful, full-blown programming language, but I frequently use it to make SMALL programs for this kind of quick automation. You can be lazy now and not to learn perl programing, or you can be lazy later after you learn perl. Who saves more time over a long run?
But it is a general, complete programming language.
e.g., automatically download sequences from genbank, run multiple sequence alignment with clustal, and reformat it to nexus file, and run it with paup. You can make a perl program, which will do all of these in one command.
Goal: Learn how to modify a script to: