Beginning Perl for Bioinformatics: An Introduction to Perl for Biologists
Начальный Perl для биоинформатики: Введение в Perl для биологов
Год издания: 2001
Автор: Tisdall James D. / Тисдалл Джеймс Д.
Издательство: O'Reilly
Язык: Английский
Формат: DjVu
Качество: Отсканированные страницы + слой распознанного текста
Количество страниц: 370
Описание:
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 output
Оглавление
Preface
1. Biology and Computer Science
2. Getting Started with Perl
3. The Art of Programming
4. Sequences and Strings
5. Motifs and Loops
6. Subroutines and Bugs
7. Mutations and Randomization
8. The Genetic Code
9. Restriction Maps and Regular Expressions
10. GenBank
11. Protein Data Bank
12. BLAST
13. Further Topics
A. Resources
B. Perl Summary
Index
