James D. Tisdall

Beginning Perl for Bioinformatics

• Broschiertes Buch

Produktbeschreibung

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 output.

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Produktdetails

• Verlag: O'Reilly Media
• Seitenzahl: 384
• Erscheinungstermin: 27. November 2001
• Englisch
• Abmessung: 238mm x 182mm x 24mm
• Gewicht: 600g
• ISBN-13: 9780596000806
• ISBN-10: 0596000804
• Artikelnr.: 09754374

Autorenporträt

James Tisdall has worked as a musician, a programmer at Bell Labs (where he programmed for speech research and discovered a formal language for musical rhythm), and as a bioinformaticist at Mercator Genetics in Menlo Park, California, and at Fox Chase Cancer Center in Philadelphia. He has a B.A. in mathematics from the City College of New York and an M.S. in computer science from Columbia University; he is working towards a Ph.D. in computer science at the University of Pennsylvania. In his spare time, Jim teaches computer music at the Settlement Music School in Philadelphia. He is also the author of O'Reilly's Beginning Perl for Bioinformatics.

Inhaltsangabe

Preface
What Is Bioinformatics?
About This Book
Who This Book Is For
Why Should I Learn to Program?
Structure of This Book
Conventions Used in This Book
Comments and Questions
Acknowledgments
Chapter 1: Biology and Computer Science
1.1 The Organization of DNA
1.2 The Organization of Proteins
1.3 In Silico
1.4 Limits to Computation
Chapter 2: Getting Started with Perl
2.1 A Low and Long Learning Curve
2.2 Perl's Benefits
2.3 Installing Perl on Your Computer
2.4 How to Run Perl Programs
2.5 Text Editors
2.6 Finding Help
Chapter 3: The Art of Programming
3.1 Individual Approaches to Programming
3.2 Edit-Run-Revise (and Save)
3.3 An Environment of Programs
3.4 Programming Strategies
3.5 The Programming Process
Chapter 4: Sequences and Strings
4.1 Representing Sequence Data
4.2 A Program to Store a DNA Sequence
4.3 Concatenating DNA Fragments
4.4 Transcription: DNA to RNA
4.5 Using the Perl Documentation
4.6 Calculating the Reverse Complement in Perl
4.7 Proteins, Files, and Arrays
4.8 Reading Proteins in Files
4.9 Arrays
4.10 Scalar and List Context
4.11 Exercises
Chapter 5: Motifs and Loops
5.1 Flow Control
5.2 Code Layout
5.3 Finding Motifs
5.4 Counting Nucleotides
5.5 Exploding Strings into Arrays
5.6 Operating on Strings
5.7 Writing to Files
5.8 Exercises
Chapter 6: Subroutines and Bugs
6.1 Subroutines
6.2 Scoping and Subroutines
6.3 Command-Line Arguments and Arrays
6.4 Passing Data to Subroutines
6.5 Modules and Libraries of Subroutines
6.6 Fixing Bugs in Your Code
6.7 Exercises
Chapter 7: Mutations and Randomization
7.1 Random Number Generators
7.2 A Program Using Randomization
7.3 A Program to Simulate DNA Mutation
7.4 Generating Random DNA
7.5 Analyzing DNA
7.6 Exercises
Chapter 8: The Genetic Code
8.1 Hashes
8.2 Data Structures and Algorithms for Biology
8.3 The Genetic Code
8.4 Translating DNA into Proteins
8.5 Reading DNA from Files in FASTA Format
8.6 Reading Frames
8.7 Exercises
Chapter 9: Restriction Maps and Regular Expressions
9.1 Regular Expressions
9.2 Restriction Maps and Restriction Enzymes
9.3 Perl Operations
9.4 Exercises
Chapter 10: GenBank
10.1 GenBank Files
10.2 GenBank Libraries
10.3 Separating Sequence and Annotation
10.4 Parsing Annotations
10.5 Indexing GenBank with DBM
10.6 Exercises
Chapter 11: Protein Data Bank
11.1 Overview of PDB
11.2 Files and Folders
11.3 PDB Files
11.4 Parsing PDB Files
11.5 Controlling Other Programs
11.6 Exercises
Chapter 12: BLAST
12.1 Obtaining BLAST
12.2 String Matching and Homology
12.3 BLAST Output Files
12.4 Parsing BLAST Output
12.5 Presenting Data
12.6 Bioperl
12.7 Exercises
Chapter 13: Further Topics
13.1 The Art of Program Design
13.2 Web Programming
13.3 Algorithms and Sequence Alignment
13.4 Object-Oriented Programming
13.5 Perl Modules
13.6 Complex Data Structures
13.7 Relational Databases
13.8 Microarrays and XML
13.9 Graphics Programming
13.10 Modeling Networks
13.11 DNA Computers
Appendix A: Resources
A.1 Perl
A.2 Computer Science
A.3 Linux
A.4 Bioinformatics
A.5 Molecular Biology
Appendix B: Perl Summary
B.1 Command Interpretation
B.2 Comments
B.3 Scalar Values and Scalar Variables
B.4 Assignment
B.5 Statements and Blocks
B.6 Arrays
B.7 Hashes
B.8 Operators
B.9 Operator Precedence
B.10 Basic Operators
B.11 Conditionals and Logical Operators
B.12 Binding Operators
B.13 Loops
B.14 Input/Output
B.15 Regular Expressions
B.16 Scalar and List Context
B.17 Subroutines and Modules
B.18 Built-in Functions
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