Beginning Perl for Bioinformatics
Beginning Perl for Bioinformatics By James Tisdall
October 2001
Pages: 384

| Table of Contents | Index | Sample Chapter | Colophon

Table of Contents

  1. Chapter 1 Biology and Computer Science

    1. The Organization of DNA

    2. The Organization of Proteins

    3. In Silico

    4. Limits to Computation

  2. Chapter 2 Getting Started with Perl

    1. A Low and Long Learning Curve

    2. Perl's Benefits

    3. Installing Perl on Your Computer

    4. How to Run Perl Programs

    5. Text Editors

    6. Finding Help

  3. Chapter 3 The Art of Programming

    1. Individual Approaches to Programming

    2. Edit—Run—Revise (and Save)

    3. An Environment of Programs

    4. Programming Strategies

    5. The Programming Process

  4. Chapter 4 Sequences and Strings

    1. Representing Sequence Data

    2. A Program to Store a DNA Sequence

    3. Concatenating DNA Fragments

    4. Transcription: DNA to RNA

    5. Using the Perl Documentation

    6. Calculating the Reverse Complement in Perl

    7. Proteins, Files, and Arrays

    8. Reading Proteins in Files

    9. Arrays

    10. Scalar and List Context

    11. Exercises

  5. Chapter 5 Motifs and Loops

    1. Flow Control

    2. Code Layout

    3. Finding Motifs

    4. Counting Nucleotides

    5. Exploding Strings into Arrays

    6. Operating on Strings

    7. Writing to Files

    8. Exercises

  6. Chapter 6 Subroutines and Bugs

    1. Subroutines

    2. Scoping and Subroutines

    3. Command-Line Arguments and Arrays

    4. Passing Data to Subroutines

    5. Modules and Libraries of Subroutines

    6. Fixing Bugs in Your Code

    7. Exercises

  7. Chapter 7 Mutations and Randomization

    1. Random Number Generators

    2. A Program Using Randomization

    3. A Program to Simulate DNA Mutation

    4. Generating Random DNA

    5. Analyzing DNA

    6. Exercises

  8. Chapter 8 The Genetic Code

    1. Hashes

    2. Data Structures and Algorithms for Biology

    3. The Genetic Code

    4. Translating DNA into Proteins

    5. Reading DNA from Files in FASTA Format

    6. Reading Frames

    7. Exercises

  9. Chapter 9 Restriction Maps and Regular Expressions

    1. Regular Expressions

    2. Restriction Maps and Restriction Enzymes

    3. Perl Operations

    4. Exercises

  10. Chapter 10 GenBank

    1. GenBank Files

    2. GenBank Libraries

    3. Separating Sequence and Annotation

    4. Parsing Annotations

    5. Indexing GenBank with DBM

    6. Exercises

  11. Chapter 11 Protein Data Bank

    1. Overview of PDB

    2. Files and Folders

    3. PDB Files

    4. Parsing PDB Files

    5. Controlling Other Programs

    6. Exercises

  12. Chapter 12 BLAST

    1. Obtaining BLAST

    2. String Matching and Homology

    3. BLAST Output Files

    4. Parsing BLAST Output

    5. Presenting Data

    6. Bioperl

    7. Exercises

  13. Chapter 13 Further Topics

    1. The Art of Program Design

    2. Web Programming

    3. Algorithms and Sequence Alignment

    4. Object-Oriented Programming

    5. Perl Modules

    6. Complex Data Structures

    7. Relational Databases

    8. Microarrays and XML

    9. Graphics Programming

    10. Modeling Networks

    11. DNA Computers

  1. Appendix A Resources

    1. Perl

    2. Computer Science

    3. Linux

    4. Bioinformatics

    5. Molecular Biology

  2. Appendix B Perl Summary

    1. Command Interpretation

    2. Comments

    3. Scalar Values and Scalar Variables

    4. Assignment

    5. Statements and Blocks

    6. Arrays

    7. Hashes

    8. Operators

    9. Operator Precedence

    10. Basic Operators

    11. Conditionals and Logical Operators

    12. Binding Operators

    13. Loops

    14. Input/Output

    15. Regular Expressions

    16. Scalar and List Context

    17. Subroutines and Modules

    18. Built-in Functions

  3. Colophon

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