Chapter 1 Biology and Computer Science
The Organization of DNA
The Organization of Proteins
In Silico
Limits to Computation
Chapter 2 Getting Started with Perl
A Low and Long Learning Curve
Perl's Benefits
Installing Perl on Your Computer
How to Run Perl Programs
Text Editors
Finding Help
Chapter 3 The Art of Programming
Individual Approaches to Programming
Edit—Run—Revise (and Save)
An Environment of Programs
Programming Strategies
The Programming Process
Chapter 4 Sequences and Strings
Representing Sequence Data
A Program to Store a DNA Sequence
Concatenating DNA Fragments
Transcription: DNA to RNA
Using the Perl Documentation
Calculating the Reverse Complement in Perl
Proteins, Files, and Arrays
Reading Proteins in Files
Arrays
Scalar and List Context
Exercises
Chapter 5 Motifs and Loops
Flow Control
Code Layout
Finding Motifs
Counting Nucleotides
Exploding Strings into Arrays
Operating on Strings
Writing to Files
Exercises
Chapter 6 Subroutines and Bugs
Subroutines
Scoping and Subroutines
Command-Line Arguments and Arrays
Passing Data to Subroutines
Modules and Libraries of Subroutines
Fixing Bugs in Your Code
Exercises
Chapter 7 Mutations and Randomization
Random Number Generators
A Program Using Randomization
A Program to Simulate DNA Mutation
Generating Random DNA
Analyzing DNA
Exercises
Chapter 8 The Genetic Code
Hashes
Data Structures and Algorithms for Biology
The Genetic Code
Translating DNA into Proteins
Reading DNA from Files in FASTA Format
Reading Frames
Exercises
Chapter 9 Restriction Maps and Regular Expressions
Regular Expressions
Restriction Maps and Restriction Enzymes
Perl Operations
Exercises
Chapter 10 GenBank
GenBank Files
GenBank Libraries
Separating Sequence and Annotation
Parsing Annotations
Indexing GenBank with DBM
Exercises
Chapter 11 Protein Data Bank
Overview of PDB
Files and Folders
PDB Files
Parsing PDB Files
Controlling Other Programs
Exercises
Chapter 12 BLAST
Obtaining BLAST
String Matching and Homology
BLAST Output Files
Parsing BLAST Output
Presenting Data
Bioperl
Exercises
Chapter 13 Further Topics
The Art of Program Design
Web Programming
Algorithms and Sequence Alignment
Object-Oriented Programming
Perl Modules
Complex Data Structures
Relational Databases
Microarrays and XML
Graphics Programming
Modeling Networks
DNA Computers
Appendix A Resources
Perl
Computer Science
Linux
Bioinformatics
Molecular Biology
Appendix B Perl Summary
Command Interpretation
Comments
Scalar Values and Scalar Variables
Assignment
Statements and Blocks
Arrays
Hashes
Operators
Operator Precedence
Basic Operators
Conditionals and Logical Operators
Binding Operators
Loops
Input/Output
Regular Expressions
Scalar and List Context
Subroutines and Modules
Built-in Functions
Colophon
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