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Contents Listing

Preface



1. Biology and Computer Science

The Organization of DNA

The Organization of Proteins

In Silico

Limits to Computation



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



3. The Art of Programming

Individual Approaches to Programming

Edit-Run-Revise (and Save)

An Environment of Programs

Programming Strategies

The Programming Process



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



5. Motifs and Loops

Flow Control

Code Layout

Finding Motifs

Counting Nucleotides

Exploding Strings into Arrays

Operating on Strings

Writing to Files

Exercises



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



7. Mutations and Randomization

Random Number Generators

A Program Using Randomization

A Program to Simulate DNA Mutation

Generating Random DNA

Analyzing DNA

Exercises



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



9. Restriction Maps and Regular Expressions

Regular Expressions

Restriction Maps and Restriction Enzymes

Perl Operations

Exercises



10. GenBank

GenBank Files

GenBank Libraries

Separating Sequence and Annotation

Parsing Annotations

Indexing GenBank with DBM

Exercises



11. Protein Data Bank

Files and Folders

PDB Files

Parsing PDB Files

Controlling Other Programs

Exercises



12. BLAST

Obtaining BLAST

String Matching and Homology

BLAST Output Files

Parsing BLAST Output

Presenting Data

Bioperl

Exercises



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



A. Resources



B. Perl Summary



Index