Blast

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.

The book is useful. Knowing BLAST is a must. This is good.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?

This book is a great protocol book for blast.But the theory part is not well organized. You may want to seek other book if you are interested in this part.

It's a good introductory book. Good explanation. Materials quality is excellent, soft cover, good price, ¡it's a Oreilly book!.Good job! thanks amazon!

I liked it, I loved it, and I want more! It's all about the Bioinformatics Tool, BLAST.

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 search2. Sequence alignment and how the algorithms work3. Blast and how the Blast statistics are calculated4. The different types of Blast e.g. WU-Blast5. Approaches to Performance speedup6. Reference sections on BLAST parametersThe 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..

Yes, this book is the only book which is describing complete information about BLAST tool. Its convenient for people which is in the area of BIOInformatics because it includes some basic knowledge of Gene!