Beginning Perl for Bioinformatics (Paperback)

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Beginning Perl for Bioinformatics (Paperback)

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內容描述

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 ContentsPreface

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