- Beginning Perl for Bioinformatics
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- A Note Regarding Supplemental Files
- Preface
- 1. Biology and Computer Science
- 2. Getting Started with Perl
- 3. The Art of Programming
- 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
- 5. Motifs and Loops
- 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
- 7. Mutations and Randomization
- 8. The Genetic Code
- 9. Restriction Maps and Regular Expressions
- 10. GenBank
- 11. Protein Data Bank
- 12. BLAST
- 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
- A. Resources
- 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
- Index
- About the Author
- Colophon
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The following conventions are used in this book:
- Italic
Used for commands, filenames, directory names, variables, modules, URLs, and for the first use of a term
-
Constant width Used in code examples and to show the output of commands
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