Mastering Perl for bioinformatics /
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ISBN：9780596003074
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简介
Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capacities in string handling, text processing, networking, and rapid prototyping, has emerged as the programming language of choice for biological data analysis. "Mastering Perl for Bioinformatics" covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with "Beginning Perl for Bioinformatics," forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics. The range of topics covered in "Mastering Perl for Bioinformatics" prepares the reader for enduring and emerging developments in critical areas of bioinformatics programming such as: Gene finding String alignment Methods of data storage and retrieval (SML and databases) Modeling of networks (graphs and Petri nets) Graphics (Tk) Parallelization Interfacing with other programming languages Statistics (PDL) Protein structure determination Biological models of computation (DNA Computers) Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.
目录
Foreword p. ix
Preface p. xi
Object-Oriented Programming in Perl
Modular Programming with Perl p. 3
What Is a Module? p. 3
Why Perl Modules? p. 3
Namespaces p. 5
Packages p. 6
Defining Modules p. 8
Storing Modules p. 9
Writing Your First Perl Module p. 11
Using Modules p. 20
CPAN Modules p. 21
Exercises p. 31
Data Structures and String Algorithms p. 33
Basic Perl Data Types p. 33
References p. 34
Matrices p. 47
Complex Data Structures p. 51
Printing Complex Data Structures p. 56
Data Structures in Action p. 58
Dynamic Programming p. 59
Approximate String Matching p. 60
Resources p. 69
Exercises p. 70
Object-Oriented Programming in Perl p. 72
What Is Object-Oriented Programming? p. 73
Using Perl Classes (Without Writing Them) p. 75
Objects, Methods, and Classes in Perl p. 80
Arrow Notation (-[right angle bracket]) p. 81
Gene1: An Example of a Perl Class p. 83
Details of the Gene1 Class p. 85
Gene2.pm: A Second Example of a Perl Class p. 93
Gene3.pm: A Third Example of a Perl Class p. 102
How AUTOLOAD Works p. 107
Cleaning Up Unused Objects with DESTROY p. 113
Gene.pm: A Fourth Example of a Perl Class p. 115
How to Document a Perl Class with POD p. 127
Additional Topics p. 129
Resources p. 129
Exercises p. 130
Sequence Formats and Inheritance p. 132
Inheritance p. 132
FileIO.pm: A Class to Read and Write Files p. 133
SeqFileIO.pm: Sequence File Formats p. 144
Resources p. 169
Exercises p. 169
A Class for Restriction Enzymes p. 173
Envisioning an Object p. 173
Rebase.pm: A Class Module p. 175
Restriction.pm: Finding Recognition Sites p. 185
Drawing Restriction Maps p. 191
Resources p. 199
Exercises p. 199
Perl and Bioinformatics
Perl and Relational Databases p. 205
One Perl, Many Databases p. 205
Popular Relational Databases p. 207
Relational Database Definitions p. 208
Structured Query Language p. 210
Administering Your Database p. 214
Relational Database Design p. 218
Perl DBI and DBD Interface Modules p. 224
A Rebase Database Implementation p. 235
Additional Topics p. 244
Resources p. 245
Exercises p. 245
Perl and the Web p. 247
How the Web Works p. 248
Web Servers and Browsers p. 255
The Common Gateway Interface p. 255
Rebase: Building Dynamic Web Pages p. 261
Exercises p. 269
Perl and Graphics p. 271
Computer Graphics p. 271
GD p. 274
Adding GD Graphics to Restrictionmap.pm p. 276
Making Graphs p. 283
Resources p. 289
Exercises p. 289
Introduction to Bioperl p. 291
The Growth of Bioperl p. 292
Installing Bioperl p. 292
Testing Bioperl p. 296
Bioperl Problems p. 303
Overview of Objects p. 304
bptutorial.pl p. 306
bptutorial.pl: sequence_manipulation Demo p. 313
Using Bioperl Modules p. 318
Appendixes
Perl Summary p. 323
Installing Perl p. 360
Index p. 369
Preface p. xi
Object-Oriented Programming in Perl
Modular Programming with Perl p. 3
What Is a Module? p. 3
Why Perl Modules? p. 3
Namespaces p. 5
Packages p. 6
Defining Modules p. 8
Storing Modules p. 9
Writing Your First Perl Module p. 11
Using Modules p. 20
CPAN Modules p. 21
Exercises p. 31
Data Structures and String Algorithms p. 33
Basic Perl Data Types p. 33
References p. 34
Matrices p. 47
Complex Data Structures p. 51
Printing Complex Data Structures p. 56
Data Structures in Action p. 58
Dynamic Programming p. 59
Approximate String Matching p. 60
Resources p. 69
Exercises p. 70
Object-Oriented Programming in Perl p. 72
What Is Object-Oriented Programming? p. 73
Using Perl Classes (Without Writing Them) p. 75
Objects, Methods, and Classes in Perl p. 80
Arrow Notation (-[right angle bracket]) p. 81
Gene1: An Example of a Perl Class p. 83
Details of the Gene1 Class p. 85
Gene2.pm: A Second Example of a Perl Class p. 93
Gene3.pm: A Third Example of a Perl Class p. 102
How AUTOLOAD Works p. 107
Cleaning Up Unused Objects with DESTROY p. 113
Gene.pm: A Fourth Example of a Perl Class p. 115
How to Document a Perl Class with POD p. 127
Additional Topics p. 129
Resources p. 129
Exercises p. 130
Sequence Formats and Inheritance p. 132
Inheritance p. 132
FileIO.pm: A Class to Read and Write Files p. 133
SeqFileIO.pm: Sequence File Formats p. 144
Resources p. 169
Exercises p. 169
A Class for Restriction Enzymes p. 173
Envisioning an Object p. 173
Rebase.pm: A Class Module p. 175
Restriction.pm: Finding Recognition Sites p. 185
Drawing Restriction Maps p. 191
Resources p. 199
Exercises p. 199
Perl and Bioinformatics
Perl and Relational Databases p. 205
One Perl, Many Databases p. 205
Popular Relational Databases p. 207
Relational Database Definitions p. 208
Structured Query Language p. 210
Administering Your Database p. 214
Relational Database Design p. 218
Perl DBI and DBD Interface Modules p. 224
A Rebase Database Implementation p. 235
Additional Topics p. 244
Resources p. 245
Exercises p. 245
Perl and the Web p. 247
How the Web Works p. 248
Web Servers and Browsers p. 255
The Common Gateway Interface p. 255
Rebase: Building Dynamic Web Pages p. 261
Exercises p. 269
Perl and Graphics p. 271
Computer Graphics p. 271
GD p. 274
Adding GD Graphics to Restrictionmap.pm p. 276
Making Graphs p. 283
Resources p. 289
Exercises p. 289
Introduction to Bioperl p. 291
The Growth of Bioperl p. 292
Installing Bioperl p. 292
Testing Bioperl p. 296
Bioperl Problems p. 303
Overview of Objects p. 304
bptutorial.pl p. 306
bptutorial.pl: sequence_manipulation Demo p. 313
Using Bioperl Modules p. 318
Appendixes
Perl Summary p. 323
Installing Perl p. 360
Index p. 369
Mastering Perl for bioinformatics /
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