ISBN-10:
0596002998
ISBN-13:
9780596002992
Pub. Date:
Publisher:
BLAST: An Essential Guide to the Basic Local Alignment Search Tool

BLAST: An Essential Guide to the Basic Local Alignment Search Tool

Paperback(First Edition)

$49.99
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Overview

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.


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Product Details

ISBN-13: 9780596002992
Publisher: O'Reilly Media, Incorporated
Publication date: 07/01/2003
Edition description: First Edition
Pages: 362
Product dimensions: 7.00(w) x 9.19(h) x 0.82(d)

About the Author

Ian Korf received his B.A. from Cornell University and his Ph.D from Indiana University. His formal training is in molecular biology but he has had a fondness for computer programming since his early teens. His post-doctoral research at Washington University in St. Louis and at The Wellcome Trust Sanger Institute in the U.K. has focused on genomic sequence analysis with an emphasis on comparative genomics and gene prediction. His goal in life is to follow genomes, wherever they happen to take him.

Mark Yandell received his PhD in Molecular, Cellular and Developmental Biology from the University of Colorado, Boulder. After graduation, he joined the Genome Sequencing Center at Washington University, where he pursued post-doctoral studies in computational biology, genome annotation and SNP discovery. In 1999 he joined Celera Genomics, where he wrote much of the software used by Celera to annotate and analyze the drosophila, human, mouse and mosquito genomes. He recently joined the Berkeley Drosophila Genome Project.

Joseph Bedell received his B.S. in Genetics from the University of Georgia in 1991 then worked on mosquito genetics at the Centers for Disease Control and Prevention in Atlanta. He went on to complete a Ph.D. in human genetics at the University of California, Irvine in 1999. Joseph, like his co-authors, completed a post-doc in mammalian gene annotation with Warren Gish, one of the original developers of BLAST. He is currently the Director of Bioinformatics for Orion Genomics in St. Louis where he spends his days (and nights) using BLAST to answer important biological and phylogenetic questions in plants.

Table of Contents


  • Forward


  • Preface


  • Introduction


    • Chapter 1: Hello BLAST




  • Theory


    • Chapter 2: Biological Sequences


    • Chapter 3: Sequence Alignment


    • Chapter 4: Sequence Similarity




  • Practice


    • Chapter 5: BLAST


    • Chapter 6: Anatomy of a BLAST Report


    • Chapter 7: A BLAST Statistics Tutorial


    • Chapter 8: 20 Tips to Improve Your BLAST Searches


    • Chapter 9: BLAST Protocols




  • Industrial-Strength BLAST


    • Chapter 10: Installation and Command-Line Tutorial


    • Chapter 11: BLAST Databases


    • Chapter 12: Hardware and Software Optimizations




  • BLAST Reference


    • Chapter 13: NCBI-BLAST Reference


    • Chapter 14: WU-BLAST Reference




  • Appendixes


    • NCBI Display Formats


    • Nucleotide Scoring Schemes


    • NCBI-BLAST Scoring Schemes


    • blast-imager.pl


    • blast2table.pl




  • Glossary


  • Colophon


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