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| Biology and Computer Science | |
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| The Organization of DNA | |
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| The Organization of Proteins | |
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| In Silico | |
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| Limits to Computation | |
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| Getting Started with Perl | |
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| A Low and Long Learning Curve | |
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| Perl's Benefits | |
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| Installing Perl on Your Computer | |
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| How to Run Perl Programs | |
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| Text Editors | |
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| Finding Help | |
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| The Art of Programming | |
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| Individual Approaches to Programming | |
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| Edit-Run-Revise (and Save) | |
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| An Environment of Programs | |
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| Programming Strategies | |
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| The Programming Process | |
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| Sequences and Strings | |
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| Representing Sequence Data | |
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| A Program to Store a DNA Sequence | |
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| Concatenating DNA Fragments | |
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| Transcription: DNA to RNA | |
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| Using the Perl Documentation | |
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| Calculating the Reverse Complement in Perl | |
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| Proteins, Files, and Arrays | |
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| Reading Proteins in Files | |
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| Arrays | |
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| Scalar and List Context | |
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| Exercises | |
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| Motifs and Loops | |
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| Flow Control | |
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| Code Layout | |
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| Finding Motifs | |
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| Counting Nucleotides | |
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| Exploding Strings into Arrays | |
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| Operating on Strings | |
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| Writing to Files | |
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| Exercises | |
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| Subroutines and Bugs | |
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| Subroutines | |
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| Scoping and Subroutines | |
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| Command-Line Arguments and Arrays | |
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| Passing Data to Subroutines | |
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| Modules and Libraries of Subroutines | |
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| Fixing Bugs in Your Code | |
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| Exercises | |
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| Mutations and Randomization | |
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| Random Number Generators | |
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| A Program Using Randomization | |
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| A Program to Simulate DNA Mutation | |
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| Generating Random DNA | |
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| Analyzing DNA | |
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| Exercises | |
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| The Genetic Code | |
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| Hashes | |
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| Data Structures and Algorithms for Biology | |
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| The Genetic Code | |
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| Translating DNA into Proteins | |
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| Reading DNA from Files in FASTA Format | |
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| Reading Frames | |
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| Exercises | |
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| Restriction Maps and Regular Expressions | |
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| Regular Expressions | |
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| Restriction Maps and Restriction Enzymes | |
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| Perl Operations | |
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| Exercises | |
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| GenBank | |
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| GenBank Files | |
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| GenBank Libraries | |
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| Separating Sequence and Annotation | |
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| Parsing Annotations | |
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| Indexing GenBank with DBM | |
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| Exercises | |
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| Protein Data Bank | |
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| Files and Folders | |
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| PDB Files | |
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| Parsing PDB Files | |
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| Controlling Other Programs | |
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| Exercises | |
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| Blast | |
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| Obtaining BLAST | |
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| String Matching and Homology | |
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| BLAST Output Files | |
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| Parsing BLAST Output | |
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| Presenting Data | |
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| Bioperl | |
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| Exercises | |
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| Further Topics | |
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| The Art of Program Design | |
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| Web Programming | |
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| Algorithms and Sequence Alignment | |
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| Object-Oriented Programming | |
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| Perl Modules | |
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| Complex Data Structures | |
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| Relational Databases | |
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| Microarrays and XML | |
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| Graphics Programming | |
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| Modeling Networks | |
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| DNA Computers | |
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| Resources | |