Beginning Perl for Bioinformatics

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• Beginning Perl for Bioinformatics
  • SPECIAL OFFER: Upgrade this ebook with OReilly
  • A Note Regarding Supplemental Files
  • Preface
    • What Is Bioinformatics?
      • What Bioinformatics Can Do
    • 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
  • 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
  • 2. Getting Started with Perl
    • 2.1. A Low and Long Learning Curve
    • 2.2. Perls Benefits
      • 2.2.1. Ease of Programming
      • 2.2.2. Rapid Prototyping
      • 2.2.3. Portability, Speed, and Program Maintenance
      • 2.2.4. Versions of Perl
    • 2.3. Installing Perl on Your Computer
      • 2.3.1. Perl May Already Be Installed!
      • 2.3.2. No Internet Access?
      • 2.3.3. Downloading
      • 2.3.4. Binary Versus Source Code
      • 2.3.5. Installation
        • 2.3.5.1. Unix and Linux
        • 2.3.5.2. Macintosh
        • 2.3.5.3. Windows
    • 2.4. How to Run Perl Programs
      • 2.4.1. Unix or Linux
      • 2.4.2. Macs
      • 2.4.3. Windows
    • 2.5. Text Editors
    • 2.6. Finding Help
  • 3. The Art of Programming
    • 3.1. Individual Approaches to Programming
    • 3.2. EditRunRevise (and Save)
      • 3.2.1. Saves and Backups
      • 3.2.2. Error Messages
      • 3.2.3. Debugging
    • 3.3. An Environment of Programs
      • 3.3.1. Open Source Programs
    • 3.4. Programming Strategies
    • 3.5. The Programming Process
      • 3.5.1. The Design Phase
      • 3.5.2. Algorithms
      • 3.5.3. Pseudocode and Code
      • 3.5.4. Comments
  • 4. Sequences and Strings
    • 4.1. Representing Sequence Data
    • 4.2. A Program to Store a DNA Sequence
      • 4.2.1. Control Flow
      • 4.2.2. Comments Revisited
      • 4.2.3. Command Interpretation
      • 4.2.4. Statements
        • 4.2.4.1. Variables
        • 4.2.4.2. Strings
        • 4.2.4.3. Assignment
        • 4.2.4.4. Print
        • 4.2.4.5. Exit
    • 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
  • 5. Motifs and Loops
    • 5.1. Flow Control
      • 5.1.1. Conditional Statements
        • 5.1.1.1. Conditional tests and matching braces
      • 5.1.2. Loops
        • 5.1.2.1. open and unless
    • 5.2. Code Layout
    • 5.3. Finding Motifs
      • 5.3.1. Getting User Input from the Keyboard
      • 5.3.2. Turning Arrays into Scalars with join
      • 5.3.3. do-until Loops
      • 5.3.4. Regular Expressions
        • 5.3.4.1. Regular expressions and character classes
        • 5.3.4.2. Pattern matching with =~ and regular expressions
    • 5.4. Counting Nucleotides
    • 5.5. Exploding Strings into Arrays
    • 5.6. Operating on Strings
    • 5.7. Writing to Files
    • 5.8. Exercises
  • 6. Subroutines and Bugs
    • 6.1. Subroutines
      • 6.1.1. Advantages of Subroutines
      • 6.1.2. Writing Subroutines
    • 6.2. Scoping and Subroutines
      • 6.2.1. Arguments
      • 6.2.2. Scoping
    • 6.3. Command-Line Arguments and Arrays
    • 6.4. Passing Data to Subroutines
      • 6.4.1. Subroutines: Pass by Value
      • 6.4.2. Subroutines: Pass by Reference
    • 6.5. Modules and Libraries of Subroutines
    • 6.6. Fixing Bugs in Your Code
      • 6.6.1. use warnings; and use strict;
      • 6.6.2. Fixing Bugs with Comments and Print Statements
      • 6.6.3. The Perl Debugger
        • 6.6.3.1. A program with bugs
        • 6.6.3.2. How to start and stop the debugger
        • 6.6.3.3. Debugger command summary
        • 6.6.3.4. Stepping through statements with the debugger
        • 6.6.3.5. Setting breakpoints
        • 6.6.3.6. Fixing another bug
        • 6.6.3.7. use warnings; and use strict; redux
    • 6.7. Exercises
  • 7. Mutations and Randomization
    • 7.1. Random Number Generators
    • 7.2. A Program Using Randomization
      • 7.2.1. Seeding the Random Number Generator
      • 7.2.2. Control Flow
      • 7.2.3. Making a Sentence
      • 7.2.4. Randomly Selecting an Element of an Array
      • 7.2.5. Formatting
      • 7.2.6. Another Way to Calculate the Random Position
    • 7.3. A Program to Simulate DNA Mutation
      • 7.3.1. Pseudocode Design
        • 7.3.1.1. Select a random position in a string
        • 7.3.1.2. Choose a random nucleotide
        • 7.3.1.3. Place a random nucleotide into a random position
      • 7.3.2. Improving the Design
      • 7.3.3. Combining the Subroutines to Simulate Mutation
      • 7.3.4. A Bug in Your Program?
    • 7.4. Generating Random DNA
      • 7.4.1. Bottom-up Versus Top-down
      • 7.4.2. Subroutines for Generating a Set of Random DNA
      • 7.4.3. Turning the Design into Code
    • 7.5. Analyzing DNA
      • 7.5.1. Some Notes About the Code
    • 7.6. Exercises
  • 8. The Genetic Code
    • 8.1. Hashes
    • 8.2. Data Structures and Algorithms for Biology
      • 8.2.1. A Gene Expression Database
      • 8.2.2. Gene Expression Data Using Unsorted Arrays
      • 8.2.3. Gene Expression Data Using Sorted Arrays and Binary Search
      • 8.2.4. Gene Expression Data Using Hashes
      • 8.2.5. Relational Databases
      • 8.2.6. DBM
    • 8.3. The Genetic Code
      • 8.3.1. Background
      • 8.3.2. Translating Codons to Amino Acids
      • 8.3.3. The Redundancy of the Genetic Code
      • 8.3.4. Using Hashes for the Genetic Code
    • 8.4. Translating DNA into Proteins
    • 8.5. Reading DNA from Files in FASTA Format
      • 8.5.1. FASTA Format
      • 8.5.2. A Design to Read FASTA Files
      • 8.5.3. A Subroutine to Read FASTA Files
      • 8.5.4. Writing Formatted Sequence Data
      • 8.5.5. A Main Program for Reading DNA and Writing Protein
    • 8.6. Reading Frames
      • 8.6.1. What Are Reading Frames?
      • 8.6.2. Translating Reading Frames
    • 8.7. Exercises
  • 9. Restriction Maps and Regular Expressions
    • 9.1. Regular Expressions
    • 9.2. Restriction Maps and Restriction Enzymes
      • 9.2.1. Background
      • 9.2.2. Planning the Program
      • 9.2.3. Restriction Enzyme Data
      • 9.2.4. Logical Operators and the Range Operator
      • 9.2.5. Finding the Restriction Sites
    • 9.3. Perl Operations
      • 9.3.1. Precedence of Operations and Parentheses
    • 9.4. Exercises
  • 10. GenBank
    • 10.1. GenBank Files
    • 10.2. GenBank Libraries
    • 10.3. Separating Sequence and Annotation
      • 10.3.1. Using Arrays
      • 10.3.2. Using Scalars
        • 10.3.2.1. Pattern modifiers
        • 10.3.2.2. Examples of pattern modifiers
        • 10.3.2.3. Separating annotations from sequence
    • 10.4. Parsing Annotations
      • 10.4.1. Using Arrays
      • 10.4.2. When to Use Regular Expressions
      • 10.4.3. Main Program
      • 10.4.4. Parsing Annotations at the Top Level
      • 10.4.5. Parsing the FEATURES Table
        • 10.4.5.1. Features
        • 10.4.5.2. Parsing
    • 10.5. Indexing GenBank with DBM
      • 10.5.1. DBM Essentials
      • 10.5.2. A DBM Database for GenBank
    • 10.6. Exercises
  • 11. Protein Data Bank
    • 11.1. Overview of PDB
    • 11.2. Files and Folders
      • 11.2.1. Opening Directories
      • 11.2.2. Recursion
      • 11.2.3. Processing Many Files
    • 11.3. PDB Files
      • 11.3.1. PDB File Format
      • 11.3.2. SEQRES
    • 11.4. Parsing PDB Files
      • 11.4.1. Extracting Primary Sequence
      • 11.4.2. Finding Atomic Coordinates
    • 11.5. Controlling Other Programs
      • 11.5.1. The Stride Secondary Structure Predictor
      • 11.5.2. Parsing Stride Output
    • 11.6. Exercises
  • 12. BLAST
    • 12.1. Obtaining BLAST
    • 12.2. String Matching and Homology
    • 12.3. BLAST Output Files
    • 12.4. Parsing BLAST Output
      • 12.4.1. Extracting Annotation and Alignments
      • 12.4.2. Parsing BLAST Alignments
    • 12.5. Presenting Data
      • 12.5.1. The printf Function
      • 12.5.2. here Documents
      • 12.5.3. format and write
    • 12.6. Bioperl
      • 12.6.1. Sample Modules
      • 12.6.2. Bioperl Tutorial Script
    • 12.7. Exercises
  • 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
      • 13.5.1. Bioperl
    • 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
  • A. Resources
    • A.1. Perl
      • A.1.1. Web Site
      • A.1.2. CPAN: Comprehensive Perl Archive Network
      • A.1.3. FAQs: Frequently Asked Questions
        • A.1.3.1. Beginners
      • A.1.4. Online Manuals
      • A.1.5. Books
      • A.1.6. Conference
      • A.1.7. Newsgroups
    • A.2. Computer Science
      • A.2.1. Algorithms
      • A.2.2. Software Engineering
      • A.2.3. Theory of Computer Science
      • A.2.4. General Programming
    • A.3. Linux
    • A.4. Bioinformatics
      • A.4.1. Books
      • A.4.2. Governmental Organizations
      • A.4.3. Conferences
    • A.5. Molecular Biology
  • B. Perl Summary
    • B.1. Command Interpretation
    • B.2. Comments
    • B.3. Scalar Values and Scalar Variables
      • B.3.1. Strings
      • B.3.2. Numbers
      • B.3.3. 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.10.1. Arithmetic Operators
      • B.10.2. Bitwise Operators
      • B.10.3. String Operators
      • B.10.4. File Test Operators
    • B.11. Conditionals and Logical Operators
      • B.11.1. true and false
      • B.11.2. Logical Operators
      • B.11.3. Using Logical Operators for Control Flow
      • B.11.4. The if Statement
    • B.12. Binding Operators
    • B.13. Loops
    • B.14. Input/Output
      • B.14.1. Input from Files
      • B.14.2. Input from STDIN
      • B.14.3. Input from Files Named on the Command Line
      • B.14.4. Output Commands
        • B.14.4.1. Output to STDOUT, STDERR, and Files
    • B.15. Regular Expressions
      • B.15.1. Overview
      • B.15.2. Metacharacters
        • B.15.2.1. Escaping with \
        • B.15.2.2. Alternation with |
        • B.15.2.3. Grouping with ( )
        • B.15.2.4. Character classes
        • B.15.2.5. Matching any character with .
        • B.15.2.6. Beginning and end of strings with ^ and $
        • B.15.2.7. Quantifiers: * + {MIN,} {MIN,MAX} ?
        • B.15.2.8. Making quantifiers match minimally with ?
      • B.15.3. Capturing Matched Patterns
      • B.15.4. Metasymbols
      • B.15.5. Extending Regular-Expression Sequences
      • B.15.6. Pattern Modifiers
    • B.16. Scalar and List Context
    • B.17. Subroutines and Modules
    • B.18. Built-in Functions
  • Index
  • About the Author
  • Colophon
  • SPECIAL OFFER: Upgrade this ebook with OReilly

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