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

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!

"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!