Books: Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics

By: James Tisdall

Publisher: O'Reilly Media, Inc.

I found this book very helpful to understand the basics of using PERL to design programs that you need, to extract or manipulate data.

If you read this book you'll be able to use your own designed programs to parse database files and extract only what you need and even analyze DNA/RNA or protein data.

Table of Contents

Copyright

Preface

What Is Bioinformatics?

About This Book

Who This Book Is For

Why Should I Learn to Program?

Structure of This Book

Conventions Used in This Book

Comments and Questions

Acknowledgments

1. Biology and Computer Science

Section 1.1. The Organization of DNA

Section 1.2. The Organization of Proteins

Section 1.3. In Silico

Section 1.4. Limits to Computation

Chapter 2. Getting Started with Perl

Section 2.1. A Low and Long Learning Curve

Section 2.2. Perl's Benefits

Section 2.3. Installing Perl on Your Computer

Section 2.4. How to Run Perl Programs

Section 2.5. Text Editors

Section 2.6. Finding Help

Chapter 3. The Art of Programming

Section 3.1. Individual Approaches to Programming

Section 3.2. Edit—Run—Revise (and Save)

Section 3.3. An Environment of Programs

Section 3.4. Programming Strategies

Section 3.5. The Programming Process

Chapter 4. Sequences and Strings

Section 4.1. Representing Sequence Data

Section 4.2. A Program to Store a DNA Sequence

Section 4.3. Concatenating DNA Fragments

Section 4.4. Transcription: DNA to RNA

Section 4.5. Using the Perl Documentation

Section 4.6. Calculating the Reverse Complement in Perl

Section 4.7. Proteins, Files, and Arrays

Section 4.8. Reading Proteins in Files

Section 4.9. Arrays

Section 4.10. Scalar and List Context

Section 4.11. Exercises

Chapter 5. Motifs and Loops

Section 5.1. Flow Control

Section 5.2. Code Layout

Section 5.3. Finding Motifs

Section 5.4. Counting Nucleotides

Section 5.5. Exploding Strings into Arrays

Section 5.6. Operating on Strings

Section 5.7. Writing to Files

Section 5.8. Exercises

Chapter 6. Subroutines and Bugs

Section 6.1. Subroutines

Section 6.2. Scoping and Subroutines

Section 6.3. Command-Line Arguments and Arrays

Section 6.4. Passing Data to Subroutines

Section 6.5. Modules and Libraries of Subroutines

Section 6.6. Fixing Bugs in Your Code

Section 6.7. Exercises

Chapter 7. Mutations and Randomization

Section 7.1. Random Number Generators

Section 7.2. A Program Using Randomization

Section 7.3. A Program to Simulate DNA Mutation

Section 7.4. Generating Random DNA

Section 7.5. Analyzing DNA

Section 7.6. Exercises

Chapter 8. The Genetic Code

Section 8.1. Hashes

Section 8.2. Data Structures and Algorithms for Biology

Section 8.3. The Genetic Code

Section 8.4. Translating DNA into Proteins

Section 8.5. Reading DNA from Files in FASTA Format

Section 8.6. Reading Frames

Section 8.7. Exercises

Chapter 9. Restriction Maps and Regular Expressions

Section 9.1. Regular Expressions

Section 9.2. Restriction Maps and Restriction Enzymes

Section 9.3. Perl Operations

Section 9.4. Exercises

Chapter 10. GenBank

Section 10.1. GenBank Files

Section 10.2. GenBank Libraries

Section 10.3. Separating Sequence and Annotation

Section 10.4. Parsing Annotations

Section 10.5. Indexing GenBank with DBM

Section 10.6. Exercises

Chapter 11. Protein Data Bank

Section 11.1. Overview of PDB

Section 11.2. Files and Folders

Section 11.3. PDB Files

Section 11.4. Parsing PDB Files

Section 11.5. Controlling Other Programs

Section 11.6. Exercises

Chapter 12. BLAST

Section 12.1. Obtaining BLAST

Section 12.2. String Matching and Homology

Section 12.3. BLAST Output Files

Section 12.4. Parsing BLAST Output

Section 12.5. Presenting Data

Section 12.6. Bioperl

Section 12.7. Exercises

Chapter 13. Further Topics

Section 13.1. The Art of Program Design

Section 13.2. Web Programming

Section 13.3. Algorithms and Sequence Alignment

Section 13.4. Object-Oriented Programming

Section 13.5. Perl Modules

Section 13.6. Complex Data Structures

Section 13.7. Relational Databases

Section 13.8. Microarrays and XML

Section 13.9. Graphics Programming

Section 13.10. Modeling Networks

Section 13.11. DNA Computers

Appendix A. Resources

Section A.1. Perl

Section A.2. Computer Science

Section A.3. Linux

Section A.4. Bioinformatics

Section A.5. Molecular Biology

Appendix B. Perl Summary

Section B.1. Command Interpretation

Section B.2. Comments

Section B.3. Scalar Values and Scalar Variables

Section B.4. Assignment

Section B.5. Statements and Blocks

Section B.6. Arrays

Section B.7. Hashes

Section B.8. Operators

Section B.9. Operator Precedence

Section B.10. Basic Operators

Section B.11. Conditionals and Logical Operators

Section B.12. Binding Operators

Section B.13. Loops

Section B.14. Input/Output

Section B.15. Regular Expressions

Section B.16. Scalar and List Context

Section B.17. Subroutines and Modules

Section B.18. Built-in Functions

Index