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Blast
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Customer Reviews
Rating:  - The most useful bioinformatics book
The O'Reilly BLAST book by Korf, Yandell and Bedell is written by people that know their subject. For anyone who wants to know what they are doing when running a BLAST search rather than simply treating it like a black box, this book is essential.
It is not perfect, however. Several phrases in the parameter section near the back of the book are not explained. MegaBLAST is correctly described as being quite different from blastn, but that difference is not made clear other than the use of query packing. The -E and -G options are not made clear in the megaBLAST section, and one must turn to the blastall pages to better understand what they do.
A second edition would be most welcome, as many improvements, changes and additions have taken place in the last few years. Discontiguous MegaBLAST, for example, was not released when this book was written.
When the book first appeared, one of my students complained that so much of the book was taken up by the parameters section. Ironically, this is the part that I have turned to the most in the time that I have had the book.
I have a shelf full of bioinformatics books in front of me right now, and I have used this book more than any of them.
Rating: - Very Practical & Useful Users Guide
From a users-perspective this book serves its purpose well - it explains what it is that BLAST is doing "under-the-hood" so that one may better customize Blast's search behavior. All I know is that I really learned a lot of basic fundamental core concepts here that I previously just took for granted.
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.
Rating: - Blast User's Bible
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
Rating:  - useful for comparative sequence alignment tasks
BLAST is a well-known tool for bioinformatics (biological sciences+computer sciences). In this book contains a concepts of central dogma of molecular biology, sequence aligment, sequece similarity, practical BLAST programs (divide into 5 programs), and how to install and use BLAST tool. Moreover, it also offers enough tips to improve my BLAST searches usage. I think this book's content is well-writing and well-organizing for comparative sequeces alignment tasks. I use this book to begin in bioinformatics and it can help me to learn about this. But this book does not contain all of things that I want to known on bioinformatics or computational biology.
Rating: - How does sequence alignment actually work?
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..
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