Datasheet

Time for a little bit of history. Before the era of bioinformatics, only two ways

of performing biological experiments were available: within a living organism

(so-called

in vivo) or in an artificial environment (so-called in vitro, from the

Latin

in glass). Taking the analogy further, we can say that bioinformatics is in

fact

in silico biology, from the silicon chips on which microprocessors are built.

This new way of doing biology has certainly become very trendy, but

don’t think that “trendy” translates into “lightweight” or “flash-in-the-pan.”

Bioinformatics goes way beyond trendy — it’s at the center of the most

recent developments in biology, such as the deciphering of the human

genome (another buzzword), “system biology” (trying to look at the global

picture), new biotechnologies, new legal and forensic techniques, as well as

the personalized medicine of the future.

Because of the centrality of bioinformatics to cutting-edge developments in

molecular biology, people from many different fields have been stumbling

across the term in a variety of different contexts. If you’re a biology, medical,

or computer science student, a professional in the pharmaceutical industry,

a lawyer or a policeman worrying about DNA testing, a consumer concerned

about GMOs (Genetically Modified Organisms), or even a NASDAQ investor

interested in start-up companies, you’ll already have come across the word

bioinformatics. If you’re good at what you do, you’ll want to know what all the

fuss is about. This chapter, then, is for you.

Instead of a formal definition that would take hours to cover all the ins and

outs of the topic, the best way to get a quick feel for what bioinformatics —

or swimming, for that matter — is all about is to jump right into the water;

that’s what we do next. Go ahead and get your feet wet with some basic mole-

cular biology concepts — and the relevant questions intimately connected

with such concepts — that all together define bioinformatics.

Analyzing Protein Sequences

If you eat steak, you’re intimately acquainted with proteins. (Your taste buds

know them intimately anyway, even if your rational mind was too busy with

dinner to master the concept.) For you non-steak lovers out there, you’ll be

pleased to know that proteins abound in fish and vegetables, too. Moreover,

all these proteins are made up of the same basic building blocks, called

amino acids. Amino acids are already quite complex organic molecules, made

of carbon, hydrogen, oxygen, nitrogen, and sulfur atoms. So the overall recipe

for a protein (the one your rational mind will appreciate, even if your taste

buds won’t) is something like C

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Part I: Getting Started in Bioinformatics

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