Fishing with a net

John Wiley & Sons, 1998. £38.95 (xiv + 384 pages)ISBN 0 47 119196 5When asked if I would be interested in reviewing a book on bioinformatics, I jumped at the opportunity. I had developed a comfortable routine for analysing DNA and protein sequences. However, I was also confident that there must be a simpler way of doing things than mine. There was a time when gene sequence analysis was considered the method of choice to enable the researcher to avoid doing a real experiment, a strategy not wasted on this reviewer. However, bioinformatics has developed into an essential tool of the molecular and cellular biologist and biochemist. With the explosive increase in DNA- and protein-sequence information that has become available over the last decade, it is almost impossible to analyse a newly discovered gene or protein confidently without performing a myriad of database searches. On the one hand, there are sequence databases that contain the genomes of entire organisms, including Saccharomyces cerevisiae, Caenorhabditis elegans and several bacteria, as well as a vast collection of mRNA sequences from a variety of expressed sequence tag (EST) libraries from both mammals and plants. On the other hand, we have the ability to quickly establish novel genetic and biochemical relationships through the use of two-hybrid analysis, micro-sequencing of purified protein complexes, and insertional mutagenesis. These techniques need to provide an investigator only with a short DNA or peptide sequence and, often within minutes, a vast array of DNA and protein sequences and biological information can be at the investigator's fingertips. Even 10 years ago, it might have taken months or years to reach such a point.This book is a wonderful primer designed to navigate the novice through the intricacies of in scripto analysis (many years ago, I heard David Botstein attribute this expression to Mark Rose and it has always seemed to me the perfect description of this technique). The accomplished gene searcher will also find this book a useful addition to their library.A great strength of Bioinformatics is its connection with the National Center for Biotechnology Information (NCBI). Many of the chapters were contributed by members of the NCBI, which is responsible for the maintenance of many of the sequence databases that we all use, but has also provided many of the most widely used tools for sequence analysis. Those of us who utilize DNA- and protein-sequence data on a routine basis long ago marked the NCBI homepage as one of our favorites. Now, Bioinformatics provides an excellent guide to virtually all aspects of protein and DNA sequence analysis with special emphasis on the many programs available free of charge from the NCBI homepage. The authors often take time to explain basic definitions and terminology that allow the reader to develop an understanding of the concepts behind the various analyses.While the details of each program are generally missing, at the end of each chapter is a list of Web sites that allows the reader to access and use virtually all of the programs discussed in that chapter. The editors appear to have made a great effort to allow any reader to perform essentially all of the analyses described without leaving their desk or spending a dime. While Bioinformatics is only 384 pages long, it was very slow reading, mostly because this reviewer was constantly itching to try out every Web site as it was mentioned. With only a few exceptions, which I blamed on my disdain for reading directions, I was able to access and utilize most of the programs described and have greatly expanded my list of favorites in Internet Explorer.While reading Bioinformatics, I was left with the feeling that one key component of sequence analysis was absent. The book provides the reader with access to the tools to carry out virtually any kind of DNA- or protein-sequence search or protein structural analysis that are freely available on the internet. However, there was no chapter devoted to any description of how to manipulate a DNA sequence easily into a protein sequence or to generate a restriction map. While such analysis might not fit under the umbrella of database analysis, it is essential to many investigators when using retrieved DNA sequence data and would be an important addition to any updated edition. Such programs are included in the Wisconsin GCG package of programs that are discussed in the book. However, these programs require a UNIX machine, making them much less accessible to the typical user than most of the other programs discussed in Bioinformatics.This complaint notwithstanding, I thoroughly enjoyed reading Bioinformatics. It provides a basic understanding of many of the concepts behind DNA- and protein-database searching as well as many important aspects of protein structural analysis. In any laboratory that routinely does these forms of analyses, Bioinformatics will provide an excellent reference to the principles of bioinformatics and for Web access to a collection of key programs.