Computational Molecular Biology: An Introduction

family databases and of their performance in characterising a new protein.Protein families are also discussed by Inge Jonassen in Chapter 7, but with an emphasis on PROSITE-type patterns rather than on the probabilistic methods discussed in previous chapters.The author describes in detail his own pattern discovery program Pratt as well as SPratt, which searches for conserved motifs in protein structures rather than sequences.The last two chapters of the book are fully practical.In Chapter 9, under the heading of `Networking for the biologist', Rob Harper discusses how to `avoid the World Wide Wait while using World Wide Web'.The recipes outlined here include the use of email servers, accelerated search sites and local servers for database searches and sequence submission.Chapter 10 by Kreil and Etzold demonstrates the use of the authors' software, SRS, for sequence retrieval and analysis, and includes several step-by-step `how-to-use' protocols as well as a technical section on installing the system locally.Both chapters are illustrated with screen captures, which are in many cases out of date, a common curse of books attempting to document the ever-changing Internet. In particular, the SRS chapter describes version 5 of SRS (version 6 is the current version). Fortunately many of the protocols can still be used with minor modi®cations, but the version change casts doubts on whether the SRS server installation instructions are still current.Overall, `Bioinformatics: Sequence, Structure and Databanks' appears to have been written with the biologist in mind rather than the computer scientist.However the book still requires more than a passing level of familiarity with UNIX command line operations, mathematical expressions and bioinformatics terminology, and readers without this familiarity are likely to ®nd it daunting in places.A glossary would certainly have been useful in this context (more useful than the list of biological reagent and equipment suppliers oddly found at the end of the book).At three pages, the index is also disappointing and does not list many important words or references: for example, the words `motif' and `pattern' in the index point only to Chapter 7, when Chapter 5 also deals extensively with the topic.Nevertheless, if you are looking for a review of current topics in protein characterisation and structure prediction, together with a useful summary of guidelines for practical analysis (and don't mind the US$115 price tag), this book is likely to be a worthwhile addition to your library.