programming-for-dummies

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The Basics of Bioinformatics
A second way to study a problem is to perform an experiment on a living
organism, such as a guinea pig or a human volunteer. Because this type of
experiment occurred on a living creature, it’s called in vivo, or in life.
Both in vitro and in vivo experiments are expensive and time-consuming.
Performing in vitro experiments requires laboratory equipment whereas performing
in vivo experiments requires live subjects.
Bioinformatics offers biologists a third way to conduct experiments — in
silico, or in silicon. Instead of using an expensive laboratory, equipment, and
living creatures, bioinformatics lets biologists conduct simulated experiments
with a computer.
What makes in silico experiments just as valid as in vitro or in vivo experiments
is that they all work with molecules. An in vitro experiment studies
molecules in a test tube, an in vivo experiment studies molecules in a live
animal, and in silico experiments study molecules as nothing more than data
inside the computer. Specifically, in silico experiments (bioinformatics) represent
molecules as strings that the computer manipulates.
By using knowledge of how different molecules interact, bioinformatics can
simulate molecular interactions, such as how a certain drug might interact
with cancer cells. This not only makes experimenting faster, but easier and
less expensive to conduct as well. After a bioinformatics experiment confirms
a certain result, biologists can go to the next step — testing actual
drugs and living cells in test tubes (in vitro) or on living creatures (in vivo).
Representing molecules
Bioinformatics manipulates molecules. Of course, biologists don’t care about
every molecule in existence, just the ones involved in life, such as proteins.
Four important molecules that biologists study are the ones that make up the
structure of deoxyribonucleic acid, or DNA. These four molecules are identified
by a single letter: Adenine (A), cytosine (C), guanine (G), and thymine (T).
When these molecules form a DNA strand, they link together in a sequence,
such as:
ACTGTTG
In a computer, such sequences of molecules can be represented as a string,
such as
$DNA = ‘ACTGTTG’;
Of course, these aren’t the only four molecules that biologists study, but the
idea is the same. Represent every molecule as a single letter and then re-create
the molecular structure as nothing more than a string.