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Title: Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition by Andreas D. Baxevanis, B. F. Francis Ouellette ISBN: 0-471-38391-0 Publisher: Wiley-Interscience Pub. Date: 06 April, 2001 Format: Paperback Volumes: 1 List Price(USD): $74.95 |
Average Customer Rating: 3.62 (13 reviews)
Rating: 5
Summary: Great book, easy to follow, expert authors
Comment: 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.
Rating: 2
Summary: Poor as an introduction to the field
Comment: 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.
Rating: 3
Summary: Somewhat more than an out-of-date catalog of tools
Comment: 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.
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Title: Bioinformatics: Sequence and Genome Analysis by David W. Mount ISBN: 0879696087 Publisher: Cold Spring Harbor Laboratory Pub. Date: 15 March, 2001 List Price(USD): $75.00 |
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Title: Developing Bioinformatics Computer Skills by Cynthia Gibas, Per Jambeck ISBN: 1565926641 Publisher: O'Reilly & Associates Pub. Date: 15 April, 2001 List Price(USD): $34.95 |
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Title: Bioinformatics for Dummies by Jean-Michel Claverie, Cedric Notredame ISBN: 0764516965 Publisher: For Dummies Pub. Date: 15 January, 2003 List Price(USD): $29.99 |
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Title: Introduction to Bioinformatics by Arthur M. Lesk ISBN: 0199251967 Publisher: Oxford University Press Pub. Date: September, 2002 List Price(USD): $37.00 |
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Title: Beginning Perl for Bioinformatics by James Tisdall ISBN: 0596000804 Publisher: O'Reilly & Associates Pub. Date: 15 October, 2001 List Price(USD): $39.95 |
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