Blast 1st Edition

9 customer reviews
ISBN-13: 063-6920002994
ISBN-10: 0596002998
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Editorial Reviews

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.

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Product Details

  • Paperback: 339 pages
  • Publisher: O'Reilly Media; 1st edition (August 8, 2003)
  • Language: English
  • ISBN-10: 0596002998
  • ISBN-13: 978-0596002992
  • Product Dimensions: 7 x 0.8 x 9.2 inches
  • Shipping Weight: 1.3 pounds (View shipping rates and policies)
  • Average Customer Review: 4.6 out of 5 stars  See all reviews (9 customer reviews)
  • Amazon Best Sellers Rank: #885,489 in Books (See Top 100 in Books)

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Customer Reviews

Most Helpful Customer Reviews

20 of 20 people found the following review helpful By Julian Cook on November 23, 2003
Format: Paperback
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.
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16 of 18 people found the following review helpful By Ian Korf on August 6, 2003
Format: Paperback
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.
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5 of 5 people found the following review helpful By wiredweird HALL OF FAMETOP 1000 REVIEWER on January 28, 2006
Format: Paperback
This is the place to start for anyone using NCBI BLAST. It's a thorough description of the various BLAST programs for nucleotides, amino acids, and codons.

The book offers a biology refresher early on, but this is aimed mainly at people with serious interest in BLAST - people who normally won't need that. Next, it discusses traditional dynamic programming alsorithms for local and global alignment. Then, in just a few pages, it summarizes the mathematical meanings and derivations of the various BLAST scores (raw scores, P-values, ane E-values). The discussion just skims the theory, but will help the reader make sense of the programs' output.

Those 75 pages set the background; the next 250 contain the real meat of the book. They cover the various BLAST programs, options, and outputs. More than that, these sections discuss setting up experiments based on BLAST, and how to deal with the problems you're likely to encounter. This could be a bit more explicit about how PSI_BLAST works (and why it sometimes doesn't), but coverage is generally strong.

A few things are weak, like emphasis on the fact that experiments aren't strictly repeatable. For example, if you exactly replicate today's test next week, even if all of the other input is identical, you might still get different (and worse) E values, since they depend on the size of the database. PSSMs get little if any discussion. Also, details about internals are weak - but this is a user's book, not an implementor's, so that's a matter of scope rather than sufficiency.

Most of the book's points are illustrated with actual output or with Perl code - the lingua franca of bioinformatics, for some reason. If you're serious about using BLAST and about understanding what it's really telling you, this is the book to own.

//wiredweird
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5 of 6 people found the following review helpful By Shih-Jon Wang on August 2, 2003
Format: Paperback
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!
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