There are thirteen chapters and two appendixes in this book. The
following provides a brief introduction:
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Chapter 1
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This chapter covers some key concepts in molecular biology, as well
as how biology and computer science fit together.
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Chapter 2
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This chapter shows you how to get Perl up and running on your
computer.
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Chapter 3
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Chapter 3 provides an overview as to how
programmers accomplish their jobs. Some of the most important
practical strategies good programmers use are explained, and where to
find answers to questions that arise while you are programming is
carefully laid out. These ideas are made concrete by brief narrative
case studies that show how programmers, given a problem, find its
solution.
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Chapter 4
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In Chapter 4 you start writing Perl programs with
DNA and proteins. The programs transcribe DNA to RNA, concatenate
sequences, make the reverse complement of DNA, read sequences data
from files, and more.
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Chapter 5
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This chapter continues demonstrating the basics of the Perl language
with programs that search for motifs in DNA or protein, interact with
users at the keyboard, write data to files, use loops and conditional
tests, use regular expressions, and operate on strings and arrays.
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Chapter 6
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This chapter extends the basic knowledge of Perl in two main
directions: subroutines, which are an important way to structure
programs, and the use of the Perl debugger, which can examine in
detail a running Perl program.
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Chapter 7
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Genetic mutations, fundamental to biology, are modelled as random
events using the random number generator in Perl. This chapter uses
random numbers to generate DNA sequence data sets, and to repeatedly
mutate DNA sequence. Loops, subroutines, and lexical scoping are also
discussed.
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Chapter 8
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This chapter shows how to translate DNA to proteins, using the
genetic code. It also covers a good bit more of the Perl programming
language, such as the hash data type, sorted and unsorted arrays,
binary search, relational databases, and DBM, and how to handle FASTA
formatted sequence data.
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Chapter 9
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This chapter contains an introduction to Perl regular expressions.
The main focus of the chapter is the development of a program to
calculate a restriction map for a DNA sequence.
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Chapter 10
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The Genetic Sequence Data Bank (GenBank) is central to modern biology
and bioinformatics. In this chapter, you learn how to write programs
to extract information from GenBank files and libraries. You will
also make a database to create your own rapid access lookups on a
GenBank library.
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Chapter 11
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This chapter develops a program that can parse Protein Data Bank
(PDB) files. Some interesting Perl techniques are encountered while
doing so, such as finding and iterating over lots of files and
controlling other bioinformatics programs from a Perl program.
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Chapter 12
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Chapter 12 develops some code to parse a BLAST
output file. Also mentioned are the Bioperl project and its BLAST
parser, and some additional ways to format output in Perl.
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Chapter 13
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Chapter 13 looks ahead to topics beyond the scope
of this book.
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Appendix A
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Collected here are resources for Perl and for bioinformatics
programming, such as books and Internet sites.
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Appendix B
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This is a summary of the parts of Perl covered in this book, plus a
little more.
