Rating: 
Summary: A survey tor tool users
Review: 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.
Rating: 
Summary: Somewhat more than an out-of-date catalog of tools
Review: 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.
Rating: 
Summary: Poor as an introduction to the field
Review: 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: 
Summary: An important contribution to a cutting edge field.
Review: 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!
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