Blast
March 10, 2010 by Bioinformatics Computational Biology
Product Description
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 most important software packages used in sequence analysis and bioinformatics. Most users of BLAST, however, seldom move beyond the program’s default parameters, and never take advantage of its full power. BLAST is the only book completely devoted to this popular suite of tools. It offers biologists, computational biology students, and bioinformatics professionals a clear understanding of BLAST as well as the science it supports. This book shows you how to move beyond the default parameters, get specific answers using BLAST, and how to interpret your results. The book also contains tutorial and reference sections covering NCBI-BLAST and WU-BLAST, background material to help you understand the statistics behind BLAST, Perl scripts to help you prepare your data and analyze your results, and a wealth of tips and tricks for configuring BLAST to meet your own research needs.
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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: 3 / 5
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: 5 / 5
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!
Rating: 5 / 5
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: 5 / 5
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: 5 / 5