About the Book
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.
Related Books
Bioinformatics Books
(Bioinformatics
Books)
Table ofContents
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
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