Beginning Perl for Bioinformatics (Paperback)

With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you're a biologist with little or no programming experience, starting out in Perl can be a challenge. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems.

Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. By the end of the book you'll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference.


The book covers:

• Programming basics and working with DNA sequences and strings
  
• Debugging your code
  
• Simulating gene mutations using random number generators
  
• Regular expressions and finding motifs in data
  
• Arrays, hashes, and relational databases
  
• Regular expressions and restriction maps
  
• Using Perl to parse PDB records, annotations in GenBank, and BLAST outp

Table of Contents

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