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Beginning Perl for Bioinformatics by James Tisdall

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Programming Strategies

In order to give you, the beginning programmer, an idea of how programming is done, let's see how an experienced programmer goes about solving problems by giving a couple of instructive case studies.

Imagine that you want to count all the regulatory elements[1] in a large chunk of DNA that you just got from the sequencing lab. You're a professional bioinformatics programmer. What do you do? There are two possible solutions: find a program or write one yourself.

It's likely there is already a perfectly good, working, and maybe even free program that does exactly what you need. Very often, you can find exactly what you need on the Web and avoid the cost and expense of reinventing the wheel. This is programming at its best—minimal work for maximal effect. It's the classic case of the experimentalist's adage: a day in the library can save you six months in the lab.

An important part of the art of programming is to keep aware of collections of programs that are available. Then you can simply use the code if it does exactly what you need, or you can take an existing program and alter it to suit your own needs. Of course, copyright laws must be observed, but much is available at no cost, especially to educational and nonprofit organizations. Most Perl module code has a copyright, but you are allowed to use it and modify it given certain restrictions. Details are available at the Perl web site and with the particular modules.

How do you find this wonderful, free, and ...

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