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

August 7, 2003

Sebastopol, CA--When Galen--the brilliant anatomist of antiquity--wrote his treatise on the movement of muscles, "De Motu Musculorum," he drew his conclusions about the human body based on his dissections of pigs, dogs, and apes. That work and his teachings on anatomical procedures guided physicians for the next fourteen hundred years. The precedent for the successful use of comparative analysis in biology has a long history and continues today as scientists employ comparative sequence analysis to understand genomes, RNAs, and proteins. BLAST, the Basic Local Alignment Search Tool, is a software package used by biologist for rapid searching of nucleotide and protein databases. Despite the adjective "Basic" in its name, BLAST is a sophisticated tool that has become the single most important piece of software in the field of bioinformatics. Most users of BLAST, however, seldom move beyond the program's default parameters to take advantage of its full power.

O'Reilly's newly released BLAST (US $39.95) by Ian Korf, Mark Yandell, and Joseph Bedell 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 and the science it supports.

"BLAST is where biology, computer science, and mathematics all come together," says coauthor Mark Yandell. "If you have a background in any of these subjects and need to learn more about bioinformatics, this book will provide a good starting point."

"We wrote the book for anyone who is interested in BLAST or bioinformatics in general," adds Ian Korf. "This includes students and professionals in any of the fields Mark mentioned, and even more distantly related fields, such as medicine and law. Bioinformatics is here to stay, and a lot of disciplines are going to need to come up to speed. BLAST is a good place to start."

"BLAST" shows readers how to move beyond the default parameters, get specific answers using BLAST, and interpret the results. The book also contains tutorial and reference sections covering NCBI-BLAST and WU-BLAST, background material that will help readers understand the statistics behind BLAST, Perl scripts to help prepare data and analyze results, and a wealth of tips and tricks for configuring BLAST for specific research needs. Some of the topics covered in the book include:

  • BLAST basics and the NCBI web interface

  • Selecting appropriate search parameters


  • 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

"BLAST" is the only comprehensive reference on this important subject, offering detailed, accurate information on optimizing BLAST searches for high-throughput sequence analysis.

Additional Resources:

  • Chapter 4, "Sequence Similarity"

  • More information about the book, including Table of Contents, index, author bios, and samples

  • A cover graphic in JPEG format

    Ian Korf, Mark Yandell, and Joseph Bedell
    ISBN 0-596-00299-8, 339 pages, $39.95 US, $61.95 CA, 28.50 UK
    1-800-998-9938; 1-707-827-7000

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