Briefings in Bioinformatics Advance Access originally published online on February 3, 2006
Briefings in Bioinformatics 2006 7(1):123-124; doi:10.1093/bib/bbk012
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Book Reviews |
Bioinformatics: A Practical Guide to the Analysis of Genes & Proteins, (third editon).
Edited by Andreas D. Baxevanis and B.F. Francis Ouellette
New York: John Wiley & Sons;
ISBN: 0471 478784; 540pp.; 2004; $79.95. In the post-genomics era of contemporary biological research, it is imperative for molecular biologists to survey and utilize bioinformatic algorithms, software tools and databases. The prosperity of bioinformatic resources in the public domain is evidently an answer to the needs of molecular biologists, which in return post new challenges and point out to new research directions for bioinformaticians, as the two fields increasingly intertwine. It is noted, however, the traditional education for molecular biologists in higher institutes deviates from that of bioinformatics, a field being more computation-driven and software-engineering-focused. Meanwhile, various research branches of bioinformatics have matured to immense complexity and great depth. The drive to bring the bioinformatic knowledge to molecular biologists therefore has become increasingly momentous, as the synergy between the two fields is to be realized and in some cases, has led to great advances in biological insights and therapeutic potentials.
This book, the third edition of a previous bestseller, is undoubtedly one of the most successful pieces of literature to bridge this gap. The book is organized in a lucid flow of five individual sections, each of which contains one or more chapters written by authoritative bioinformatic experts. The first part presents an overview of a plethora of biological databases, with interesting details of the history of some of the most popular sequence databases, as well as many well-designed examples of the usage of a number of databases covering sequences, genomes, biomedical research and so on. Part two brings us a more numerical topic of the analysis at the nucleotide level, in which gene prediction methods are described in reasonable detail and other methods (e.g. promoter predictions) were covered by concise overviews. The newly added chapters in this edition also include predictive methods using RNA sequences and an overview of sequence polymorphisms and their usage, which are nice supplements, in my view. The third part deals with the intricacies of analysis at the protein level. Protein structure prediction and analysis are beautifully laid out, along with the protein interaction databases and biological pathway databases. Compared with the previous section of the nucleotide-based analysis, these chapters include more systems-related information, which I would recommend anyone interested in Systems Biology to read, although the coverage is bit scattered and uneven considering the broadness of the topics. Part four is the most comprehensive one among the five and includes a suit of seven different topics dedicated to a number of important computational concepts and methods to infer biological relationships. Highlights of this part include the chapter of the Phylogenetic Analysis and the chapter of Proteomics and Protein Identification. The chapters cover the basic concepts and tools in these areas in reasonable details and provide very practical guidance for bioinformatic users to navigate the complexity of the analysis tools. The last part helps those interested in computer programming to sample some basic skills in Perl, for Perl is the most popular language used by bioinformaticians, and is relatively easy to start with as a first programming language for many molecular biologists.
This book is a gem to read and use in practice not only for molecular biologists, but also for many well-versed chemists, computer scientists, engineers, mathematicians and physicists who work in the cross-disciplinary fields of biology. As a bioinformatic scientist, I find this book serves as a well-organized reference, covers many important concepts of computational biology, and leads us into an amazing wealth of bioinformatic tools and information on the web. Baxevanis and Ouellette did an excellent job to make a seemingly daunting book such a nice easy-read.
Principal Research Scientist, Integrative Biology, Eli Lilly and Company, Greenfield, IN 46140, USA
Submitted: July 20, 2005. Received (in revised form): July 22, 2005.
CiteULike 
Connotea 
Del.icio.us What's this?
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||