Beginning Perl for Bioinformatics

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; Chapter 1: Biology and Computer Science; 1.1 The Organization of DNA; 1.2 The Organization of Proteins; 1.3 In Silico; 1.4 Limits to Computation; Chapter 2: Getting Started with Perl; 2.1 A Low and Long Learning Curve; 2.2 Perl's Benefits; 2.3 Installing Perl on Your Computer; 2.4 How to Run Perl Programs; 2.5 Text Editors; 2.6 Finding Help; Chapter 3: The Art of Programming; 3.1 Individual Approaches to Programming; 3.2 Edit???Run???Revise (and Save); 3.3 An Environment of Programs; 3.4 Programming Strategies; 3.5 The Programming Process; Chapter 4: Sequences and Strings; 4.1 Representing Sequence Data; 4.2 A Program to Store a DNA Sequence; 4.3 Concatenating DNA Fragments; 4.4 Transcription: DNA to RNA; 4.5 Using the Perl Documentation; 4.6 Calculating the Reverse Complement in Perl; 4.7 Proteins, Files, and Arrays; 4.8 Reading Proteins in Files; 4.9 Arrays; 4.10 Scalar and List Context; 4.11 Exercises; Chapter 5: Motifs and Loops; 5.1 Flow Control; 5.2 Code Layout; 5.3 Finding Motifs; 5.4 Counting Nucleotides; 5.5 Exploding Strings into Arrays; 5.6 Operating on Strings; 5.7 Writing to Files; 5.8 Exercises; Chapter 6: Subroutines and Bugs; 6.1 Subroutines; 6.2 Scoping and Subroutines; 6.3 Command-Line Arguments and Arrays; 6.4 Passing Data to Subroutines; 6.5 Modules and Libraries of Subroutines; 6.6 Fixing Bugs in Your Code; 6.7 Exercises; Chapter 7: Mutations and Randomization; 7.1 Random Number Generators; 7.2 A Program Using Randomization; 7.3 A Program to Simulate DNA Mutation; 7.4 Generating Random DNA; 7.5 Analyzing DNA; 7.6 Exercises; Chapter 8: The Genetic Code; 8.1 Hashes; 8.2 Data Structures and Algorithms for Biology; 8.3 The Genetic Code; 8.4 Translating DNA into Proteins; 8.5 Reading DNA from Files in FASTA Format; 8.6 Reading Frames; 8.7 Exercises; Chapter 9: Restriction Maps and Regular Expressions; 9.1 Regular Expressions; 9.2 Restriction Maps and Restriction Enzymes; 9.3 Perl Operations; 9.4 Exercises; Chapter 10: GenBank; 10.1 GenBank Files; 10.2 GenBank Libraries; 10.3 Separating Sequence and Annotation; 10.4 Parsing Annotations; 10.5 Indexing GenBank with DBM; 10.6 Exercises; Chapter 11: Protein Data Bank; 11.1 Overview of PDB; 11.2 Files and Folders; 11.3 PDB Files; 11.4 Parsing PDB Files; 11.5 Controlling Other Programs; 11.6 Exercises; Chapter 12: BLAST; 12.1 Obtaining BLAST; 12.2 String Matching and Homology; 12.3 BLAST Output Files; 12.4 Parsing BLAST Output; 12.5 Presenting Data; 12.6 Bioperl; 12.7 Exercises; Chapter 13: Further Topics; 13.1 The Art of Program Design; 13.2 Web Programming; 13.3 Algorithms and Sequence Alignment; 13.4 Object-Oriented Programming; 13.5 Perl Modules; 13.6 Complex Data Structures; 13.7 Relational Databases; 13.8 Microarrays and XML; 13.9 Graphics Programming; 13.10 Modeling Networks; 13.11 DNA Computers; Appendix A: Resources; A.1 Perl; A.2 Computer Science; A.3 Linux; A.4 Bioinformatics; A.5 Molecular Biology; Appendix B: Perl Summary; B.1 Command Interpretation; B.2 Comments; B.3 Scalar Values and Scalar Variables; B.4 Assignment; B.5 Statements and Blocks; B.6 Arrays; B.7 Hashes; B.8 Operators; B.9 Operator Precedence; B.10 Basic Operators; B.11 Conditionals and Logical Operators; B.12 Binding Operators; B.13 Loops; B.14 Input/Output; B.15 Regular Expressions; B.16 Scalar and List Context; B.17 Subroutines and Modules; B.18 Built-in Functions; Colophon;