Beginning Perl for Bioinformatics (Paperback)

James Tisdall

  • 出版商: O'Reilly
  • 出版日期: 2001-11-27
  • 定價: $1,400
  • 售價: 9.5$1,330
  • 貴賓價: 8.8$1,232
  • 語言: 英文
  • 頁數: 400
  • 裝訂: Paperback
  • ISBN: 0596000804
  • ISBN-13: 9780596000806
  • 相關分類: Perl 程式語言生物資訊 Bioinformatics
  • 立即出貨 (庫存 < 3)

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商品描述

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 Contents

Preface

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

商品描述(中文翻譯)

Perl因其在數據中檢測模式的高度發展能力而成為生物數據分析中最受歡迎的語言之一。但是,如果你是一位沒有或幾乎沒有編程經驗的生物學家,開始學習Perl可能會是一個挑戰。許多生物學家在學習如何將該語言應用於生物信息學時遇到困難。最受歡迎的Perl編程書籍通常對非編程生物學家來說過於理論化,過於專注於計算機科學,無法解決非常具體的問題。

《生物信息學Perl入門》旨在通過將編程視為一項重要的新實驗室技能,快速幫助您克服Perl語言的障礙,展示在實驗室中立即有用的Perl程序和技術。每一章都專注於解決特定的生物信息學問題或問題類型,從最簡單的問題開始,隨著書籍的進展而增加複雜性。每一章都包含編程練習,並通過展示和修改處理各種實際生物問題的程序來教授生物信息學。通過閱讀本書,您將對Perl基礎有扎實的理解,擁有一系列用於解析BLAST和GenBank等任務的程序,並具備進一步進行高級生物信息學編程的技能。本書的後幾章更詳細地關注特定的生物信息學主題。本書適用於課堂教學、自學和作為參考書。

本書內容包括:
- 編程基礎和處理DNA序列和字符串
- 調試代碼
- 使用隨機數生成器模擬基因突變
- 正則表達式和在數據中查找模式
- 數組、哈希和關聯數據庫
- 正則表達式和限制圖譜
- 使用Perl解析PDB記錄、GenBank中的註釋和BLAST輸出

目錄:
- 前言
- 第1章 生物學和計算機科學
- 第2章 開始使用Perl
- 第3章 編程的藝術
- 第4章 序列和字符串
- 第5章 模式和循環

以上是本書的部分內容,涵蓋了Perl在生物信息學中的應用。本書適用於課堂教學、自學和作為參考書籍。