Book description
Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capacities in string handling, text processing, networking, and rapid prototyping, has emerged as the programming language of choice for biological data analysis.Mastering Perl for Bioinformatics covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with Beginning Perl for Bioinformatics, forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics.The range of topics covered in Mastering Perl for Bioinformatics prepares the reader for enduring and emerging developments in critical areas of bioinformatics programming such as:
- Gene finding
- String alignment
- Methods of data storage and retrieval (SML and databases)
- Modeling of networks (graphs and Petri nets)
- Graphics (Tk)
- Parallelization
- Interfacing with other programming languages
- Statistics (PDL)
- Protein structure determination
- Biological models of computation (DNA Computers)
Table of contents
- A Note Regarding Supplemental Files
- Foreword
- Preface
-
I. Object-Oriented Programming in Perl
- 1. Modular Programming with Perl
-
2. Data Structures and String Algorithms
- Basic Perl Data Types
- References
- Matrices
- Complex Data Structures
- Printing Complex Data Structures
- Data Structures in Action
- Dynamic Programming
- Approximate String Matching
- Resources
- Exercises
-
3. Object-Oriented Programming in Perl
- What Is Object-Oriented Programming?
- Using Perl Classes (Without Writing Them)
- Objects, Methods, and Classes in Perl
- Arrow Notation (->)
- Gene1: An Example of a Perl Class
- Details of the Gene1 Class
- Gene2.pm: A Second Example of a Perl Class
- Gene3.pm: A Third Example of a Perl Class
- How AUTOLOAD Works
- Cleaning Up Unused Objects with DESTROY
- Gene.pm: A Fourth Example of a Perl Class
- How to Document a Perl Class with POD
- Additional Topics
- Resources
- Exercises
- 4. Sequence Formats and Inheritance
- 5. A Class for Restriction Enzymes
-
II. Perl and Bioinformatics
- 6. Perl and Relational Databases
- 7. Perl and the Web
- 8. Perl and Graphics
- 9. Introduction to Bioperl
-
III. Appendixes
-
A. Perl Summary
- Command Interpretation
- Comments
- Scalar Values and Scalar Variables
- Assignment
- Statements and Blocks
- Arrays
- Hashes
- Complex Data Structures
- Operators
- Operator Precedence
- Basic Operators
- Conditionals and Logical Operators
- Binding Operators
- Loops
- Input/Output
- Regular Expressions
- Scalar and List Context
- Subroutines
- Modules and Packages
- Object-Oriented Programming
- Built-in Functions
- B. Installing Perl
-
A. Perl Summary
- Index
- About the Author
- Colophon
- Copyright
Product information
- Title: Mastering Perl for Bioinformatics
- Author(s):
- Release date: September 2003
- Publisher(s): O'Reilly Media, Inc.
- ISBN: 9780596003074
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