Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition
By addebook • Jun 21st, 2008 • Category: Biology •
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Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition
By Andreas D. Baxevanis, B. F. Francis Ouellette
Publisher: Wiley-Interscience
Number Of Pages: 488
Publication Date: 2001-04-06
ISBN-10 / ASIN: 0471383910
ISBN-13 / EAN: 9780471383918
Binding: Paperback
“In this book, Andy Baxevanis and Francis Ouellette . . . have undertaken the difficult task of organizing the knowledge in this field in a logical progression and presenting it in a digestible form. And they have done an excellent job. This fine text will make a major impact on biological research and, in turn, on progress in biomedicine. We are all in their debt.”-Eric Lander from the Foreword
Reviews from the First Edition
“…provides a broad overview of the basic tools for sequence analysis … For biologists approaching this subject for the first time, it will be a very useful handbook to keep on the shelf after the first reading, close to the computer.”-Nature Structural Biology
“…should be in the personal library of any biologist who uses the Internet for the analysis of DNA and protein sequence data.” -Science
“…a wonderful primer designed to navigate the novice through the intricacies of in scripto analysis … The accomplished gene searcher will also find this book a useful addition to their library … an excellent reference to the principles of bioinformatics.”-Trends in Biochemical Sciences
This new edition of the highly successful Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins provides a sound foundation of basic concepts, with practical discussions and comparisons of both computational tools and databases relevant to biological research.
Equipping biologists with the modern tools necessary to solve practical problems in sequence data analysis, the Second Edition covers the broad spectrum of topics in bioinformatics, ranging from Internet concepts to predictive algorithms used on sequence, structure, and expression data. With chapters written by experts in the field, this up-to-date reference thoroughly covers vital concepts and is appropriate for both the novice and the experienced practitioner. Written in clear, simple language, the book is accessible to users without an advanced mathematical or computer science background. This new edition includes:
* All new end-of-chapter Web resources, bibliographies, and problem sets
* Accompanying Web site containing the answers to the problems, as well as links to relevant Web resources
* New coverage of comparative genomics, large-scale genome analysis, sequence assembly, and expressed sequence tags
* A glossary of commonly used terms in bioinformatics and genomics
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition is essential reading for researchers, instructors, and students of all levels in molecular biology and bioinformatics, as well as for investigators involved in genomics, positional cloning, clinical research, and computational biology.
Summary: Not a very useful textbook at all
Rating: 3
I agree with the reviewer who said that this book is poorly organized. Actually, I would summarise this book with a single saying: TMI (Too Much Information)! In teaching you how to accomplish a simple task, the details given are tremendous, so much so that you can’t see the forest from the trees and you end up having to navigate the bioinformatics Web sites by trial and error anyway. Perhaps this book would be useful for a post-doc or someone already very familiar with those sites and want to know how they work. For the student (undergrad through Master), I suggest picking up the short-n-sweet paperback ‘Bioinformatics’ by Westhead, Parish & Twyman instead.
Summary: Bent edges
Rating: 3
Book came quickly but edges were bent, not like a new book. Returned it and got full refund.
Summary: Somewhat more than an out-of-date catalog of tools
Rating: 3
The book is a collection of chapters by different authors addressing software tools for various problems: database search, multiple sequence alignment, gene prediction, protein structure prediction, etc. A big flaw is that all of the authors assume a different level of prior background and have rather different emphases.
I’d have to agree with the other reviewer that Chapters 1 & 17, which constitute 10% of the book, are wasted paper. No one in 2001 (when the book was published), let alone 2004, needs Chapter 1’s lengthy explanation of what e-mail and web browsers are. And the perl program at the anticlimax of Chapter 17 was … anticlimactic.
The book is to a great extent a catalog of available software tools. With the exception of the chapters on multiple alignment and phylogeny, the emphasis is on not on how the tools work but how to operate them — to the of saying “at this URL there is a web page where you can either paste in your sequence or upload a file”. The idea of invoking a program through a Unix command line is more than once presented as a truly daunting prospect. The authors generally do a good job of emphasizing that the programs are the beginning of analysis and not the end; the results must always be viewed somewhat skeptically with an expert eye.
If you’re coming at the book as a biologist, you will probably find it to be a useful catalog of software, though undoubtedly dated by now. If you’re coming at it from the informatics side, you’re going to need some background… a book like Dwyer’s, Setubal and Meidanis’s, or Mount’s will get you up to speed on the algorithm aspects of the field with simplified versions of many of the big problems. Then you can look at this book to find good pointers to the ways the real-world versions have been addressed.
The book was published three years ago and, being to a large extent an index of the work of others, is necessarily no longer up to date in a fast-moving field. It needs a revision and, in the meantime, it would make more sense to snag a used copy than to pay full price for a new book.
Summary: A survey for tool users
Rating: 4
Like any survey, it seems to touch the major features only. And, as others have pointed out, the tools change but the book doesn’t.
I think this is a good, brief introduction to the wide variety of bioinformatic tools and databases on the internet. It describes the major features of each, and the kinds of results that each tool is good for. After that, the serious user will go to the sources of each tool or database, to learn more about the specifics as of the moment. No book can hope to keep up with the weekly enhancements at the major repositories.
I emphasize that this is for tools users, not tool makers. It addresses the working scientists who already know their subjects and their needs. This skips over the algorithms in favor of higher level descriptions, and skips over many of the biological reasons for the tools described. Better-informed tool users get better answers from the tools, true. At some point, though, the biologists want to skip the theory, skip the introduction to subjects in which they’re experts, and get on with their science. I don’t think this book was ever meant for people - and I’m one - who want full details of the algorithms.
I agree, the book treats its many subjects in a shallow way. I think that is by intent, since the book’s real goal is breadth and its target is a reader who knows the basic science. It’s a bit off the center of my interests, but I’ve found it helpful.
Summary: Bioinformatic for the beginner…
Rating: 4
I guess that everybody interrested by this kind of book knows already a little about bioinformatic and wants to improve his bioinformatician skill. So forget about this book:
This is really a well-documented introduction to all the methods currently used by every biologist or biology student, such as Blast, Clustal, multiple alignement or use of web-interface for submiting sequence.
So get it if you need a clear introduction to the field, but if you already know a little bit about bioinfo, immediately choose a more detailed book.
Free download Links
http://rapidshare.com/files/120594174/0471383910.rar
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