Mastering Perl for Bioinformatics [Electronic resources] نسخه متنی

Chapter 2. Data Structures and String Algorithms

So far in this book, I've used the standard Perl
data structures of scalars, arrays, and hashes. However, it is often
necessary to handle data with a more complex structure than what
those basics allow. For instance, it is frequently useful to have a
two-dimensional array.

In this chapter, you'll learn how to define and use
references and complex data
structures. After you learn the fundamentals,
you'll apply the new techniques to implement a
biologically important algorithm. These techniques are also
fundamental to the implementation of object-oriented programming, as
you'll see in Chapter 3.

The algorithm we'll study is called
approximate string matching. It lets you find
the closest match for a peptide fragment in a protein, for instance.
It uses an algorithmic technique called dynamic
programming, an essential tool for many similar biological
tasks, such as aligning biological sequences. In this chapter,
you'll see how Perl references can be used to write
programs for data problems with more complex relationships.
References are also used for the objects of object-oriented
programming.