Bioinformatics for Dummies FROM OUR EDITORS
The Barnes & Noble Review
Once upon a time, there were only two ways to perform biological experiments: within living organisms (in vivo) and within artificial environments such as glass test tubes (in vitro).
"Once upon a time" wasn't that long ago. But for those in the field, it seems like forever. There's been a massive revolution in biological research: a revolution driven by truly breathtaking amounts of data. (Think of the Human Genome Project, which generated so much information -- some 10 terabytes worth -- that Microsoft used it as unassailable proof of its enterprise database's scalability.) At the same time, an entirely new experimental method has arisen to accompany (and often replace) in vivo and in vitro approaches: "in silico" experiments performed entirely via computer models.
An entirely new field has sprung up to gather, store, analyze, and integrate the colossal amounts of data now generated in biological experimentation -- and apply that data to discovering and developing new medicines. That field, which integrates molecular biology with computer science, is called bioinformatics.
Virtually everyone who works (or plans to work) in biological science, research, or biomedicine will need to understand the field's new tools. (As will many on the "edges" of the field, such as investors and venture capitalists, lawyers interested in DNA testing, even educated citizens interested in biomedical research and genetically modified food.) There's now a book for them: Bioinformatics for Dummies.
Unlike some purely "academic" treatments of the topic, this one's written clearly enough for anyone familiar with college-level biology. It also does an exceptionally good job of answering the most important questions biological professionals ask about bioinformatics. For instance: Which is the right tool for my problem? What's the best way to use it? How do I interpret the results?
It's also extremely reliable -- no surprise, considering that its authors are two of the world's leading bioinformatics experts. Jean-Michel Claverie is Research Director at the French National Center for Scientific Research (CNRS), founder and leader of the Structural & Genomic Information Laboratory in Marseilles, reviewing editor for Science, and a leading biotech consultant (for Incyte and others). Coauthor Cﾽdric Notredame has taught bioinformatics for a decade, and led the development of T-Coffee, a remarkably accurate package for aligning multiple nucleotide or amino acid sequences -- one of the field's most important and difficult tasks.
They begin with an overview of the field and an introduction to two core bioinformatics applications: the analysis of protein and DNA/RNA sequences. Unsurprisingly, these topics recur constantly throughout the book, as the authors introduce the key tools and resources available to the professional. These include PubMed (which contains more than 11 million MEDLINE citations, going back to the '60s); Expasy, a world-leading resource for protein information; and the GenBank and LocusLink nucleotide sequence databases, to name just a few.
Claverie and Notredame focus on the areas of analysis which bioinformatics is likely to be most useful. That's still an enormous amount of information.
If you're working with protein sequences, for example, you'll learn how to retrieve protein sequences from databases; compute amino-acid composition, molecular weight, isoelectric point, and other parameters; predict antigenic sites, elements of secondary structure, and domain organization; classify proteins into families; discover their evolutionary relationships; even predict and visualize their 3-D structures.
Those working with entire genomes will learn how to browse human and animal genomes; analyze sequences in relation to specific genomes; parse microbial and eukaryotic genome sequences; find repeats, and even discover "unknown" genes.
The book offers just enough background in molecular biology to give you a clear context for the techniques it covers. It contains practical tips and techniques for improving your proficiency at sequence analysis and many other key skills. It covers Windows GUI–based tools that often have shorter learning curves -- as well as traditional Unix tools. There's even a glossary -- to demystify any jargon the authors haven't already cleared up in this exceptionally lucid book. Bill Camarda
Bill Camarda is a consultant, writer, and web/multimedia content developer. His 15 books include Special Edition Using Word 2000 and Upgrading & Fixing Networks for Dummies, Second Edition.
FROM THE PUBLISHER
Whether you're baffled by bioinformatics or just weary of wandering the Web, you've come to the right place. This friendly volume is like chatting with the experts. You'll get bioinformatics basics plus a cookbook of cool ideas, tips on tools, directions to the best Web sites, and shortcuts to great results -- all in plain English!
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