What Is Bioinformatics?

Biological data is proliferating rapidly. Public databases such as GenBank and the Protein Data Bank have been growing exponentially for some time now. With the advent of the World Wide Web and fast Internet connections, the data contained in these databases and a great many special-purpose programs can be accessed quickly, easily, and cheaply from any location in the world. As a consequence, computer-based tools now play an increasingly critical role in the advancement of biological research.

Bioinformatics, a rapidly evolving discipline, is the application of computational tools and techniques to the management and analysis of biological data. The term bioinformatics is relatively new, and as defined here, it encroaches on such terms as "computational biology" and others. The use of computers in biology research predates the term bioinformatics by many years. For example, the determination of 3D protein structure from X-ray crystallographic data has long relied on computer analysis. In this book I refer to the use of computers in biological research as bioinformatics. It's important to be aware, however, that others may make different distinctions between the terms. In particular, bioinformatics is often the term used when referring to the data and the techniques used in large-scale sequencing and analysis of entire genomes, such as C. elegans, Arabidopsis, and Homo sapiens.

What Bioinformatics Can Do

Here's a short example of bioinformatics in action. Let's say you have discovered a very interesting segment of mouse DNA and you suspect it may hold a clue to the development of fatal brain tumors in humans. After sequencing the DNA, you perform a search of Genbank and other data sources using web-based sequence alignment tools such as BLAST. Although you find a few related sequences, you don't get a direct match or any information that indicates a link to the brain tumors you suspect exist. You know that the public genetic databases are growing daily and rapidly. You would like to perform your searches every day, comparing the results to the previous searches, to see if anything new appears in the databases. But this could take an hour or two each day! Luckily, you know Perl. With a day's work, you write a program (using the Bioperl module among other things) that automatically conducts a daily BLAST search of Genbank for your DNA sequence, compares the results with the previous day's results, and sends you email if there has been any change. This program is so useful that you start running it for other sequences as well, and your colleagues also start using it. Within a few months, your day's worth of work has saved many weeks of work for your community. This example is taken from real life. There are now existing programs you can use for this purpose, even web sites where you can submit your DNA sequence and your email address, and they'll do all the work for you!

This is only a small example of what happens when you apply the power of computation to a biological problem. This is bioinformatics.