BLAST (Paperback)
Ian Korf, Mark Yandell, Joseph Bedell
- 出版商: O'Reilly Media
- 出版日期: 2003-08-08
- 售價: $1,696
- 貴賓價: $1,611
- 語言: 英文
- 頁數: 339
- 裝訂: Paperback
- ISBN: 0596002998
- ISBN-13: 9780596002992
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商品描述
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