BLAST

by Ian Korf

Book Overview

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...

• Format: Paperback
• Language: English
• ISBN: 0596002998
• ISBN13: 9780596002992
• Release Date: September 2003
• Publisher: O'Reilly Media
• Length: 339 Pages
• Weight: 1.60 lbs.
• Dimensions: 0.8" x 7.0" x 9.2"

Customer Reviews

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.

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

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 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..

Author comments

As the first reviewer mentioned, the book is not a fast read. In orderto run BLAST properly one must understand how and why it works. BLASTexists at the intersection of molecular biology, computer science, andstatistics. This might sound intimidating, but once you read about thesetopics in chapters 2-4, you'll see that it isn't so complicated and itall fits together nicely. We know that BLAST users come from a varietyof backgrounds and we have therefore written the book for a generalaudience. As a result, the book is more than just a BLAST manual, it'salso a friendly introduction to computational molecular biology.Writing this book took a lot of time and effort. It went through somepainful transformations. The authors waged many battles againstthemselves and each other to bring to you the kind of book we wished wecould have bought several years ago. We'll feel our work was justifiedif you approach your next BLAST search as a scientific experiment andnot a Google search. And if we've helped some of you to embark on a newcareer/hobby in bioinformatics, drop us a line, it's sure to make ourday.

This IS a book about BLAST!

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!