- 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: 4.5 out of 5 stars See all reviews (11 customer reviews)
- Amazon Best Sellers Rank: #314,941 in Books (See Top 100 in Books)
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Blast 1st Edition
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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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Top customer reviews
The book discusses the biology, statistics, algorithms, and computer science issues involved in explaining blast. I liked this approach because it does not head super far into any one core area but rather sticks to a strong fundamental overview of each topic. The other strong aspect of this book is that the author thoroughly compares NCBI and WU Blast throughout, characterizing instances where one may choose one over the other and/or how to tweak the parameters for both in those situations.
I orginally bought the book b/c I wanted an overview on PAM and BLOSUM matrices and to understand how Blast Statistics work. It really served as an informative contextual tutorial that has definitely raised my overall understanding on not only Blast, but to better grasp the very interdisciplinary nature concerning sequence alignment for in-silico biological research.
The book is poorly written and organized. The language is vague. Explanations are too short and incomprehensible for a new user. In explaining new concepts authors often use some unknown professional terms and notions, which they never explain. I could guess some terms after reading several times, but too much you have to guess. Some letters in formulas are not explained. Authors should have thought more about their readers.
Maybe this is a book for those who already know the subject, but it claims to be a comprehensive introduction. Also the authors claim that it is a book not for mathematicians. Having a background in statistics I have big problems understanding the material. Maybe that's exactly what they mean by "not for mathematician" - saying some words without adequate definitions?
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..
Most recent customer reviews
to run BLAST properly one must understand how and why it works.Read more