Sequence Analysis in a Nutshell (Paperback)

Darryl Leon, Scott Markel, Lorrie LeJeune

Sequence Analysis in a Nutshell (Paperback)
  • 出版商: O'Reilly
  • 出版日期: 2003-03-04
  • 定價: $1,050
  • 售價: 2.8 折 $299
  • 語言: 英文
  • 頁數: 336
  • 裝訂: Paperback
  • ISBN: 059600494X
  • ISBN-13: 9780596004941
  • 相關分類: 生物資訊 Bioinformatics、Data Science

    • 立即出貨 (庫存=1)

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商品描述

Gene sequence data is the most abundant type of data available, and if you're interested in analyzing it, you'll find a wealth of computational methods and tools to help you. In fact, finding the data is not the challenge at all; rather it is dealing with the plethora of flat file formats used to process the sequence entries and trying to remember what their specific field codes mean. If you survive by surrounding yourself with well-thumbed hard copies of readme files or remembering exactly where to look for the details when you need them, then Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases is for you. This book is a handy resource, as well as an invaluable reference, for anyone who needs to know about the practical aspects and mechanics of sequence analysis.

Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis. The book is partitioned into three fundamental areas to help you maximize your use of the content. The first section, "Databases" contains examples of flatfiles from key databases (GenBank, EMBL, SWISS-PROT), the definitions of the codes or fields used in each database, and the sequence feature types/terms and qualifiers for the nucleotide and protein databases.

The second section, "Tools" provides the command line syntax for popular applications such as ReadSeq, MEME/MAST, BLAST, ClustalW, and the EMBOSS suite of analytical tools. The third section, "Appendixes" concentrates on information essential to understanding the individual components that make up a biological sequence. The tables in this section include nucleotide and protein codes, genetic codes, as well as other relevant information.

Written in O'Reilly's enormously popular, straightforward "Nutshell" format, this book draws together essential information for bioinformaticians in industry and academia, as well as for students. If sequence analysis is part of your daily life, you'll want this easy-to-use book on your desk.

Table of Contents

Preface 


I. Data Formats


1. FASTA Format

2. GenBank/EMBL/DDBJ

3. SWISS-PROT

4. Pfam

5. PROSITE


 
 
II. Tools


6. Readseq

7. BLAST

8. BLAT

9. ClustalW

10. HMMER

11. MEME/MAST

12. EMBOSS


 

 
III. Appendixes


A. Nucleotide and Amino Acid Tables

B. Genetic Codes

C. Resources

D. Future Plans

Index

商品描述(中文翻譯)

基因序列資料是最豐富的資料類型之一，如果你有興趣進行分析，你會發現有許多計算方法和工具可以幫助你。事實上，找到資料並不是挑戰，真正的挑戰是處理用於處理序列條目的各種扁平文件格式，並試圖記住它們特定的字段代碼的含義。如果你靠著周圍擁有翻閱過的自述文件的硬拷貝或者記住需要時確切查找詳細信息的位置來生存，那麼《序列分析入門：常用工具和數據庫指南》就是為你而設的。這本書是一個方便的資源，也是一個寶貴的參考，適用於任何需要了解序列分析的實際方面和機制的人。

《序列分析入門：常用工具和數據庫指南》匯集了所有關於最常用的數據庫、分析工具和表格的重要信息。該書分為三個基本部分，以幫助你充分利用內容。第一部分“數據庫”包含了來自關鍵數據庫（GenBank、EMBL、SWISS-PROT）的扁平文件示例，每個數據庫中使用的代碼或字段的定義，以及核苷酸和蛋白質數據庫的序列特徵類型/術語和限定詞。

第二部分“工具”提供了流行應用程序（如ReadSeq、MEME/MAST、BLAST、ClustalW和EMBOSS套件）的命令行語法。第三部分“附錄”集中於理解生物序列組成部分所必需的信息。本部分的表格包括核苷酸和蛋白質代碼、遺傳代碼以及其他相關信息。

這本書以O'Reilly廣受歡迎的直接易懂的“Nutshell”格式撰寫，為工業和學術界的生物信息學家以及學生提供了必要的信息。如果序列分析是你日常生活的一部分，你一定會想要這本易於使用的書放在你的桌上。

目錄：
前言
I. 資料格式
1. FASTA格式
2. GenBank/EMBL/DDBJ
3. SWISS-PROT
4. Pfam
5. PROSITE

II. 工具
6. Readseq
7. BLAST
8. BLAT
9. ClustalW
10. HMMER
11. MEME/MAST
12. EMBOSS

III. 附錄
A. 核苷酸和氨基酸表格
B. 遺傳代碼
C. 資源
D. 未來計劃
索引

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