Blast (Paperback)

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Editorial Reviews

Product Description

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.

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.

Product Details

• Paperback: 339 pages
• Publisher: O'Reilly Media; 1st edition (June 1, 2003)
• Language: English
• ISBN-10: 0596002998
• ISBN-13: 978-0596002992
• Product Dimensions: 9.1 x 7 x 0.9 inches
• Shipping Weight: 1.3 pounds (View shipping rates and policies)
• Average Customer Review: 4.7 out of 5 stars  See all reviews (7 customer reviews)
• Amazon.com Sales Rank: #360,118 in Books (See Bestsellers in Books)

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Customer Reviews

Most Helpful Customer Reviews

17 of 17 people found the following review helpful:

5.0 out of 5 stars How does sequence alignment actually work?, November 23, 2003

By	Julian Cook (Philadelphia, PA United States) - See all my reviews (REAL NAME)

If you want to understand the nuts and bolts of how sequence alignment works, then this is the book for you. It will be especially useful for BLAST users who want to understand how it actually works and also for developers who don't know much biology, struggle with the math, but have no problem reading a perl script.

The book is basically divided into:
0. A Foreword by Stephen Altschul (the co-creator of BLAST)
1. A quick web intro to a BLAST search
2. Sequence alignment and how the algorithms work
3. Blast and how the Blast statistics are calculated
4. The different types of Blast e.g. WU-Blast
5. Approaches to Performance speedup
6. Reference sections on BLAST parameters

The real key is that this book neatly splits the difference between academic texts and papers which are quite often too difficult to read without sufficient background (and they are not precise about the implementation anyway) and the user-manual type texts which don't discuss the theory at all.

One of the best chapters (in my view) is chapter three, where they explain and illustrate the workings of the Needleman-Wunsch and Smith-Waterman algorithms for global and local alignment. If you read the text, then study and run the included perl code, you WILL understand how they work, but be prepared to spend several hours trying different examples. The real advantage of this approach is that you get a deep, practical understanding of how alignment actually works, that you just can't get from reading a mathematical treatment of the subject. Once you understand this chapter, you are actually sufficiently expert to get inside alignment code and modify it for your own purposes.

Ian Korf does continually emphasize that the algorithms may look clever, but they are, in the end, robotic in that they will quite happily align complete rubbish if you are not careful about controlling the algorithm and thinking carefully about the results you get.

There are a couple of mistakes in the diagrams (chap 3), that are addressed in the errata, but the perl code is correct.

Finally, because this book is about BLAST, it doesn't mention other methods of sequence alignment such as Hidden-Markov Models or methods of multiple sequence alignment. Perhaps they'll do a book on those as well one day..

13 of 14 people found the following review helpful:

5.0 out of 5 stars Author comments, August 6, 2003

By	Ian Korf - See all my reviews (REAL NAME)

As the first reviewer mentioned, the book is not a fast read. In order
to run BLAST properly one must understand how and why it works. BLAST
exists at the intersection of molecular biology, computer science, and
statistics. This might sound intimidating, but once you read about these
topics in chapters 2-4, you'll see that it isn't so complicated and it
all fits together nicely. We know that BLAST users come from a variety
of backgrounds and we have therefore written the book for a general
audience. As a result, the book is more than just a BLAST manual, it's
also a friendly introduction to computational molecular biology.

Writing this book took a lot of time and effort. It went through some
painful transformations. The authors waged many battles against
themselves and each other to bring to you the kind of book we wished we
could have bought several years ago. We'll feel our work was justified
if you approach your next BLAST search as a scientific experiment and
not a Google search. And if we've helped some of you to embark on a new
career/hobby in bioinformatics, drop us a line, it's sure to make our
day.

4 of 4 people found the following review helpful:

5.0 out of 5 stars This IS a book about BLAST!, August 2, 2003

By	Shih-Jon Wang (Taiwan) - See all my reviews (REAL NAME)

Useful book for biologists to understand computer algorithm. This book is very helpful if you are going through endless BLAST search. It is not a fast read but it is packed with useful information. I have started using the suggested examples and tricks in this book and feel more comfortable at doing the search. Important book for Bioinformatics researchers!