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

By Andreas D. Baxevanis and Francis B.F. Ouellette

Book Overview

"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.

• Format: Paperback
• Language: English
• ISBN: 0471383910
• ISBN13: 9780471383918
• Release Date: April 2001
• Publisher: Wiley-Interscience
• Length: 504 Pages
• Weight: 2.00 lbs.
• Dimensions: 10.0" x 0.9" x 7.0"

Customer Reviews

Great book, easy to follow, expert authors

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.

Excellent Broad-Based Coverage

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.

The Best Bioinformatics Book I've Bought

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!

from NATURE STRUCTURAL BIOLOGY review (Dec 99)

"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

An important contribution to a cutting edge field.

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!