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Beginning Perl for Bioinformatics by James Tisdall

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Data Structures and Algorithms for Biology

Biologists explore biological data and try to figure out how to do things with it based on its existing structure in living systems. Bioinformatics is often used to model that existing structure as closely as possible. (Bear with me; I'm speaking in generalities!)

Bioinformatics also can take a slightly different approach. It thinks about what it wants to do with the data and then tries to figure out how to organize it to accomplish that goal. In other words, it tries to produce an algorithm by representing the data in a convenient data structure.

Now that you've got the three datatypes of Perl in hand—namely scalars, arrays, and hashes—it's time to take a look at these interrelated topics of algorithms and data structures. We've already talked about algorithms in Chapter 3. The present discussion highlights the importance of the organization of the data for algorithms, in other words, the data structures for the algorithm.

The most important point here is that different algorithms often require different data structures.

A Gene Expression Database

Let's consider a typical problem. Say you're studying an organism that has a total of about 30,000 genes. (Yep, you're right, it's human.) Say you're looking at a type of cell that's never been well characterized under certain interesting environmental conditions, and you are determining, for each gene, whether it's being expressed.[1] You have a nice microarray facility that has given you the ...

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