오늘 포스팅은 생물정보학을 위한 Perl에 관한 두 가지 책을 써보도록 하겠습니다.
소개할 책은 "올챙이 책" 과 "개구리 책" 입니다.
올챙이 책의 경우 "펄로 시작하는 바이오인포매틱스" 라는 한국어 번역서가 있다는 점 참고하시기를 바랍니다.
Beginning Perl for Bioinformatics (올챙이 책)
Mastering Perl for Bioinformatics (개구리 책)
Beginning 을 올챙이로, Mastering을 개구리로 표지를 꾸민 것이 상당히 흥미롭습니다.
제목: Beginning Perl for Bioinformatics
저자: James Tisdall
ISBN: 0596000804
표지:
목차:
목차:
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 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
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
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
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
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
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
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
9. Restriction Maps and Regular Expressions
9.1 Regular Expressions
9.2 Restriction Maps and Restriction Enzymes
9.3 Perl Operations
9.4 Exercises
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
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
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
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
A. Resources
A.1 Perl
A.2 Computer Science
A.3 Linux
A.4 Bioinformatics
A.5 Molecular Biology
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
제목: Mastering Perl for Bioinformatics
저자: James Tisdall
ISBN: 0596003072
표지:
목차:
Part I: Object-Oriented Programming in Perl
Chap 1. Modular Programming with Perl
1.1 What is a Module?
1.2 Why Perl Modules?
1.3 Namespaces
1.4 Packages
1.5 Defining Modules
1.6 Storing Modules
1.7 Writing Your First Perl Modules
1.8 Using Modules
1.9 CPAN Mudules
1.10 Exercises
Chap2. Data Structures and String Algorithms
2.1 Basic Perl Data Types
2.2 References
2.3 Matrices
2.4 Complex Data Structures
2.5 Printing Complex Data Structures
2.6 Data Structures in Action
2.7 Dynamic Programming
2.8 Approximate String Matching
2.9 Resources
2.10 Exercises
Chap3. Object-Oriented Programming in Perl
3.1 What is Object-Oriented Programming?
3.2 Using Perl Classes (Without Writing Them)
3.3 Objects, Methods, and Classes in Perl
3.4 Arrow Notation (->)
3.5 Gene1: An Example of a Perl Class
3.6 Details of the Gene1 Class
3.7 Gene2.pm: A Second Example of a Perl Class
3.8 Gene3.pm: A Third Example of a Perl Class
3.9 How AUTOLOAD Works
3.10 Cleaning Up Unused Objects with DESTROY
3.11 Gene.pm: A Fourth Example of a Perl Class
3.12 How to Document a Perl Class with POD
3.13 Additional Topics
3.14 Resources
3.15 Exercises
Chap4. Sequence Formats and Inheritance
4.1 Inheritance
4.2 FileIO.pm: A Class to Read and Write Files
4.3 SeqFileIO.pm: Sequence File Formats
4.4 Resources
4.5 Exercises
Chap5. A Class for Restriction Enzymes
5.1 Envisioning an Object
5.2 Rebase.pm: A Class Module
5.3 Restriction.pm: Finding Recognition Sites
5.4 Drawing Restriction Maps
5.5 Resources
5.6 Exercises
Part II: Perl and Bioinformatics
Chap6. Perl and Relational Databases
6.1 One Perl, Many Databases
6.2 Popular Relational Databases
6.3 Relational Database Definitions
6.4 Structured Query Language
6.5 Structured Query Language
6.6 Relational Database Design
6.7 Perl DBI and DBD Interface Modules
6.8 A Rebase Database Implementation
6.9 Additional Topics
6.10 Resources
6.11 Exercises
Chap7. Perl and the Web
7.1 How the Web Works
7.2 Web Servers and Browsers
7.3 The Common Gateway Interface
7.4 Rebase: Building Dynamic Web Pages
7.5 Exercises
Chap8. Perl and Graphics
8.1 Computer Graphics
8.2 GD
8.3 Adding GD Graphics to Restrictionmap.pm
8.4 Making Graphs
8.5 Resources
8.6 Exercises
Chap9. Introduction to Bioperl
9.1 The Growth of Bioperl
9.2 Installing Bioperl
9.3 Testing Bioperl
9.4 Bioperl Problems
9.5 Overview of Objects
9.6 bptutorial.pl
9.7 bptutorial.pl: sequence manipulation Demo
9.8 Using Bioperl Modules
Part III: Appendixes
Appendix A. Perl Summary
1. Command Interpretation
2. Comments
3. Sclar Values and Sclar Variables
4. Assignment
5. Statements and Blocks
6. Arrays
7. Hashes
8. Complex Data Structures
9. Operators
10. Operator Precedence
11. Basic Operators
12. Conditionals and Logical Operators
13. Binding Operators
14. Loops
15. Input/Output
16. Regular Expressions
17. Sclar and List Context
18. Subroutines
19. Modules and Packages
20. Object-Oriented Programming
21. Built-in Functions
Appendix B. Installing Perl
1. Installing Perl on Your Computer
2. Bersions of Perl
3. Internet Access
4. Downloading
5. How to Run Perl Programs
6. Finding Help
참고 링크:
http://www.amazon.com/Beginning-Perl-Bioinformatics-James-Tisdall/dp/0596000804
http://www.amazon.com/Mastering-Perl-Bioinformatics-James-Tisdall/dp/0596003072
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