Mastering Perl for Bioinformatics [Electronic resources] نسخه متنی

Organization of This Book

Here's a quick summary of what the book covers. If
you're still relatively new to Perl you may want to
work through the chapters in order. If you have some programming
experience and are looking for ways to approach problems in
bioinformatics with Perl, feel free to skip around.

Part I

Chapter 1

Modules are the
standard Perl way of "packaging"
useful programs so that other programmers can easily use previous
work. Such standard modules as CGI, for instance, put the power of
interactive web site programming within reach of a programmer who
knows basic Perl. Also discussed in later chapters are Bioperl, for
manipulating biological data, and DBI, for gaining access to
relational databases. Modules are sometimes considered the most
important part of Perl because that's where a lot of
the functionality of Perl has been placed. In this chapter I show how
to write your own modules, as well as how to find useful modules and
use them in your programs.

Chapter 2

Complex data
structures and references are fundamentally important to Perl. The
basic Perl data structures of scalar, array, and hash go a long way
toward solving many (perhaps most) Perl programming problems.
However, many commonly used data structures such as multidimensional
arrays, for instance, require more sophisticated Perl data structures
to handle them. Perl enables you to define quite complex data
structures, and we'll see how all that works.

String algorithms are standard
techniques used in bioinformatics for finding important data in
biological sequences; with them, you can compare two sequences, align
two or more sequences, assemble a collection of sequence fragments,
and so forth. String algorithms underlie many of the most commonly
used programs in biology research, such as BLAST. In this chapter, a
string matching algorithm that finds the closest match to a motif,
based on the technique of dynamic programming, is presented in the
form of a working Perl program.

Chapter 3

Object-oriented programming is a
standard approach to designing programs. I assume, as a prerequisite,
that you are familiar with the programming style called declarative
programming. (For example, C and FORTRAN are declarative; C++ and
Java are object-oriented; Perl can be either.) It's
important for the Perl programmer to be familiar with the
object-oriented approach. For instance, modules are usually defined
in an object-oriented manner.

This chapter presents, step by step, the concepts and techniques of
object-oriented Perl programming, in the context of a module that
defines a simple class for keeping track of genes.

Chapter 4

In this chapter, object-oriented programming is further explored in
the context of developing software to convert sequence files to
alternate formats (FASTA, GCG, etc.). The concept of class
inheritance is introduced and implemented.

Chapter 5

This chapter further develops object-oriented programming by writing
a class that handles Rebase restriction enzyme data, a class that
calculates restriction maps, and a class that draws restriction maps.

Part II

Chapter 6

Relational
databases are important in programming because they save, organize,
and retrieve data sets. This chapter introduces relational databases
and the SQL language and includes information on designing and
administering databases. I take a close look at how one such
relational database management system, the popular MySQL, is used
from the Perl language.

Chapter 7

Web programming is one of
Perl's areas of strength. In this chapter, I start
an example that puts a laboratory up on the Web using Perl and the
CGI module. The software developed in previous chapters for
restriction mapping is made accessible from the Web.

Chapter 8

Using computer graphics to display data is one of the most important
programming skills in bioinformatics. In this chapter, graphics
programs are used to dynamically display the output of restriction
maps and data presented as graphs on the Web. The Perl module GD is
discussed and used to generate maps on the fly from web page queries.

Chapter 9

Bioperl is a set of
modules used by Perl programmers to write bioinformatics
applications. In this chapter you'll see an
introduction of the Bioperl project. Bioperl is open source (free
under a very nonrestrictive copyright) and developed by a group of
volunteers, many based in supportive research organizations. In
recent years it has achieved critical mass and is now adequately
documented and fairly broad in scope. If you do Perl bioinformatics
programming, you should certainly be aware of what Bioperl has to
offer, to avoid reinventing the wheel.

Part III

Appendix A

This appendix summarizes the parts of Perl we've
covered.

Appendix B

This appendix outlines how to install Perl.