BLAST (Paperback)

Ian Korf, Mark Yandell, Joseph Bedell

  • 出版商: O'Reilly
  • 出版日期: 2003-09-02
  • 售價: $1,790
  • 貴賓價: 9.5$1,701
  • 語言: 英文
  • 頁數: 339
  • 裝訂: Paperback
  • ISBN: 0596002998
  • ISBN-13: 9780596002992
  • 海外代購書籍(需單獨結帳)

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商品描述

Sequence similarity is a powerful tool for discovering biological function. Just as the ancient Greeks used comparative anatomy to understand the human body and linguists used the Rosetta stone to decipher Egyptian hieroglyphs, today we can use comparative sequence analysis to understand genomes. BLAST (Basic Local Alignment Search Tool), is a sophisticated software package for rapid searching of nucleotide and protein databases. It is one of the most important software packages used in sequence analysis and bioinformatics. Most users of BLAST, however, seldom move beyond the program's default parameters, and never take advantage of its full power.

BLAST is the only book completely devoted to this popular suite of tools. It offers biologists, computational biology students, and bioinformatics professionals a clear understanding of BLAST as well as the science it supports. This book shows you how to move beyond the default parameters, get specific answers using BLAST, and how to interpret your results. The book also contains tutorial and reference sections covering NCBI-BLAST and WU-BLAST, background material to help you understand the statistics behind BLAST, Perl scripts to help you prepare your data and analyze your results, and a wealth of tips and tricks for configuring BLAST to meet your own research needs. Some of the topics covered include:

  • BLAST basics and the NCBI web interface
  • How to select appropriate search parameters
  • BLAST programs: BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX, PHI-BLAST, and PSI BLAST
  • Detailed BLAST references, including NCBI-BLAST and WU-BLAST
  • Understanding biological sequences
  • Sequence similarity, homology, scoring matrices, scores, and evolution
  • Sequence Alignment
  • Calculating BLAST statistics
  • Industrial-strength BLAST, including developing applications with Perl and BLAST


BLAST is the only comprehensive reference with detailed, accurate information on optimizing BLAST searches for high-throughput sequence analysis. This is a book that any biologist should own.

Table of Contents

Foreword

Preface

Part I. Introduction

1. Hello BLAST

Part II. Theory

2. Biological Sequences

3. Sequence Alignment

4. Sequence Similarity

Part III. Practice

5. BLAST

6. Anatomy of a BLAST Report

7. A BLAST Statistics Tutorial

8. 20 Tips to Improve Your BLAST Searches

9. BLAST Protocols

Part IV. Industrial-Strength BLAST

10. Installation and Command-Line Tutorial

11. BLAST Databases

12. Hardware and Software Optimizations

Part V. BLAST Reference

13. NCBI-BLAST Reference

14. WU-BLAST Reference

Part VI. Appendixes

A. NCBI Display Formats

B. Nucleotide Scoring Schemes

C. NCBI-BLAST Scoring Schemes

D. blast-imager.pl

E. blast2table.pl

Glossary

Index

商品描述(中文翻譯)

序列相似性是發現生物功能的強大工具。就像古希臘人使用比較解剖學來理解人體,語言學家使用羅塞塔石碑來解讀埃及象形文字一樣,今天我們可以使用比較序列分析來理解基因組。BLAST(Basic Local Alignment Search Tool)是一個用於快速搜索核苷酸和蛋白質數據庫的複雜軟件包。它是序列分析和生物信息學中最重要的軟件包之一。然而,大多數BLAST的用戶很少超出程序的默認參數,從未充分利用其功能。

《BLAST》是唯一一本完全致力於這個受歡迎工具套件的書籍。它為生物學家、計算生物學學生和生物信息學專業人士提供了對BLAST及其支持的科學的清晰理解。本書向您展示如何超越默認參數,使用BLAST獲得具體答案,以及如何解釋結果。該書還包含教程和參考部分,涵蓋了NCBI-BLAST和WU-BLAST,幫助您理解BLAST背後的統計學知識,提供Perl腳本來幫助您準備數據和分析結果,以及豐富的配置BLAST以滿足您自己研究需求的技巧和訣竅。其中一些涵蓋的主題包括:

- BLAST基礎知識和NCBI網絡界面
- 如何選擇適當的搜索參數
- BLAST程序:BLASTN、BLASTP、BLASTX、TBLASTN、TBLASTX、PHI-BLAST和PSI BLAST
- 詳細的BLAST參考資料,包括NCBI-BLAST和WU-BLAST
- 理解生物序列
- 序列相似性、同源性、評分矩陣、分數和進化
- 序列對齊
- 計算BLAST統計數據
- 強大的BLAST,包括使用Perl和BLAST開發應用程序

《BLAST》是唯一一本詳細、準確地優化BLAST搜索以進行高通量序列分析的綜合參考書。這是任何生物學家都應該擁有的一本書。

目錄:

前言
前言
第一部分:介紹
1. 你好,BLAST
第二部分:理論
2. 生物序列
3. 序列對齊
4. 序列相似性
第三部分:實踐
5. BLAST
6. BLAST報告的解剖學
7. BLAST統計教程
8. 改進BLAST搜索的20個技巧
9. BLAST協議
第四部分:強大的BLAST
10. 安裝和命令行教程
11. BLAST數據庫
12. 硬件和軟件優化
第五部分:BLAST參考
13. NCBI-BLAST參考
14. WU-BLAST參考
第六部分:附錄
A. NCBI顯示格式
B. 核苷酸評分方案
C. NCBI-BLAST評分方案
D. blast-imager.pl
E. blast2table.pl
詞彙表
索引