Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition

by Andreas D. Baxevanis, B. F. Francis Ouellette

Publisher: Wiley-Interscience
ISBN: 0471383910

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Book Description

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

From Book News, Inc.

Presents fourteen chapters on tools and databases used in bioinformatics, loosely defined as the intersection of molecular and computational biology. With the goal of helping the reader design and implement a successful sequence analysis strategy, topics covered include: using software and Internet resources, submitting DNA sequences to databases, information retrieval from databases, phylogenetic analysis, a database for genome information called ACeDB, and practical aspects of multiple sequence alignment.

From the Publisher

"A useful introduction to biologists, with a particularly strong introduction to the tools available from the NCBI." (Russ B. Altman, MD, PhD, Stanford University Medical Center).

Book Reviews

• "... a useful resource to help biologists extract the maximum value from their data." - Cell
• "... 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 ... sequence data." - Science
• "... a wonderful primer designed to navigate the novice through the intricacies of in scripto analysis." - Trends in Biochemical Sciences
• "an excellent reference to the principles of bioinformatics." - TIBS
• "... a nice overview of bioinformatics that is suitable for the neophyte and those experienced in the field." - Biotech Software and Internet Report
• "... should be included in the collection of anyone involved with the emerging field of b$ - Biotech Software and Internet Report
• "...a good practical book and many will benefit from reading it." - Proteomics, No.1 2001

About the Author

Andy Baxevanis is the Associate Director for Intramural Research and the Director, Computational Genomics, at the National Human Genome Research Institute, National Institutes of Health. He received his B.S. in biological sciences from Cornell University in 1984 and his Ph.D. in the Department of Biology at The Johns Hopkins University in 1991. His research focuses on protein structure-function relationships, positional cloning, and the development of new methods for the analysis of gene expression data. His accomplishments have been recognized by the Bodossaki Foundation in Greece, who awarded him their 1999 Academic Prize in Medicine and Biology.

Francis Ouellette is Director of the Bioinformatics Core Facility at the Center for Molecular Medicine and Therapeutics, The University of British Columbia, and the Director of Bioinformatics for the Canadian Genetic Diseases Network. He previously held the position of GenBank Coordinator for the National Center for Biotechnology Information at the National Institutes of Health. He earned his B.Sc. in the Department of Biology at McGill University in 1991, and is the founder and moderator of bionet.molbio.yeast, a Usenet discussion forum for the yeast genomics community.

Excerpted from Bioinformatics : A Practical Guide to the Analysis of Genes and Proteins by Andreas D. Baxevanis, B. F. Francis Ouellette. Copyright © 2001. Reprinted by permission. All rights reserved

"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)

Customer Reviews

Although the book is presented as an introduction to the topic, its organization assumes that the reader has already been working in the area. Two of the chapters (1 and 17) are a waste of space. The first chapter presents a (useless) introduction to internet, while chapter 17 attempts (and fails to do so) to explain Perl in the context of bioinformatics. For the same money you can find far better books in the market. The good thing is that I only borrowed the book :)

I used the Baxevanis volume in coursework at Johns Hopkins Biotechnology program...several of the chapter authors are associated with the school. There's no doubt that the editor and authors are experts in their fields, but the volume seems somewhat dated, and is disjointed. I found a couple of the chapters virtually unreadable. The real killer is the price. The book is GROSSLY overpriced...

The purpose of the book appears to be to provide a broad overview of current public bioinformatics tools. If one is interested to find pointers to software that addresses a specific bioinformatics question, the book does a reasonable job of showing what was available at the end of 2000. However, this approach has two major shortcomings. First, the principles and main scientific ideas associated with each covered area are only glossed over. Second, there is a chronic lack of depth in the presentation of any particular method. Because of these two problems the book is useless to the novice and makes a poor choice as a textbook for an introductory bioinformatics course. The best chapter is #14 on phylogenetic analysis, which emphasizes the strategies of data analysis and potential misinterpretations of the results. An embarrassing addition to the second edition is a chapter on Perl, which I doubt will be useful to any type of reader. Another chapter, which would have been better left out is #1, an introduction to the internet. It may have been appropriate for the first edition, but the material is too simplistic for the present.

Five stars, a great place for people like me (trained as a biochemist) to start in a field that I know is going to be more and more important as to how I do my work in the future. I've been able to use basic things like BLAST more effectively, and finally understand that there are other ways to look at sequence besides BLAST and how to apply those tools to my own sequences. I really like the Entrez chapter, since Entrez does so much more than I ever realized it could do! I haven't ventured into the advanced territory yet (like microarrays), but at least I understand what I'm hearing in seminars now and what all those red and green spots actually represent.

I read the review by "a reader in Cambridge, MA", and don't understand what their beef is with this title. The authors have tried (and have succeeded) in pointing the readers to the best PUBLIC DOMAIN software out there, augmenting documentation that's generally lacking. Have you ever tried finding good docs on the NCBI Web site? Well, these two editors got them for you. UNIX-centric? I can't speak for the first edition, but check out the second edition and see that there's tons of Netscape screen dumps demonstrating the tools and making things as easy as possible for the reader. I originally bought this because of the reviews published in Science and Cell and a slew of other journals, all favorable, so the "reader in Cambridge" seems out of step with all of the published journal reviews of the book. Everyone's entitled to their opinion, but I just wanted to point this out for a sense of balance here, especially since my own experience was so different.

I own both the first and second editions of this book, and really think they're great. The second edition really is a brand-new book, seeing how far this field has come in a short period of time, with a lot of new material in the second edition, like on sequence assembly, comparative genomics, and BioPerl. Looking at the chapters that have been retained from the first edition, there has been extensive rewrites -- pretty impressive for a "new edition" that's now almost 100 pages thicker than the first edition was.

I also like how the second edition broadens out to resources available throughout the world, using a wider set of authors (meaning well beyond NCBI) than the first edition did. Baxevanis and Ouellette seem to have a very good sense not just for where the field is, but where the field is going, and who the major players are -- the inclusion of a chapter on whole-genome analysis (microarrays) is evidence of that, material that doesn't appear in any of the other available titles, to my knowledge.

I can see how an advanced reader interested in the mathematics underlying commonly-used bioinformatics technqiues would move to a title like Durbin et al., and these two books really are the "best in class" -- start with the Baxevanis title, and move onto the Durbin title from there. They're really the only two you'll need. I personally don't know anyone who's been disappointed by these two books.

I've looked at quite a few of the books in the field, but this one really stands head-and-shoulders above the rest. The people putting the book together are the experts in the field, and often are the ones who developed the techniques or the strategies that more and more of us depend on in trying to analyze our sequence data -- if you're gonna learn, might as well learn from the experts. The practical nature of the book has been very helpful to me in my work, striking a nice balance between the theory and practice -- some of the other books are either too mathematical or too hand-wavy. I also appreciate having the problem sets at the ends of the chapters, so I can see if I actually understood what I read. If I were teaching, I could easily see this making a really nice textbook. In Eric Lander's forward, the authors are given high marks and praise -- if he thinks so, then that's good enough for me!

A great introduction to bioinformatics with links to biological databases and data mining tools. I have the edition that was written in 1998 so many of the links in the book are now inactive. The book contains good introductory summaries of the algorithms used in the data mining tools discussed. The book however is aimed more at the biologist with little computer knowledge. If you are a computer scientist, the book will be a little boring and I would recommend "Biological Sequence Analysis" by Durbin et al. The price of the book is steep for the amount of pages you are paying for. If price is a consideration in your purchase, I recommend the use of the tutorials on many of the bioinformatics websites such as NCBI, EBI, and Swiss-Prot which are just as good as the book.

"The novice user of bioinformatics tools needs a guide that answers several fundamental questions - what are these tools designed for and what can they do; what are their limitations; how does one access them, and where can one find further information. For each of the basic sub-fields of bioinformatics, Bioinformatics provides a survey, a list of world wide web addresses (URLs), and a list of monographs and reviews to which the reader may go for further information. Each chapter covers fundamental definitions and makes no assumptions about prior knowledge.... The book provides a broad overview of the basic tools for sequence analysis. It is a good starting point for the reader who wants to learn about the types of tools used in bioinfomatics and how to get started. 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." --Terry Gaasterland, The Rockefeller University

This book represents an very important contribution to the emerging field of bioinformatics. There is a vast, and continually growing, amount of resources available for the analysis of DNA and protein sequences. The difficulty comes is making in sense of all it all, and organizing it in the most productive manner possible. This work is one of the few texts -- and certainly the most current -- to address this issue and provide realistic and usable systems to accomplish that. It should be required reading for anyone wishing to remain up-to-date in this rapidly changing field. This is one "practical guide" that really is!