What makes up a full English brekkie?

Modern Genetic Analysis - Introduction to Bioinformatics - An Introduction to Computational Biochemistry - Instant Notes
April 25, 2003

Elucidation of the DNA sequences of whole genomes has seen a huge increase in the use of computer programs to archive and analyse sequence information, providing insights into gene and protein functions, genome evolution and enabling accelerated disease gene identification. Both databases and sophisticated analytical software can be accessed via the worldwide web, making it possible for anyone to venture into the world of bioinformatics.

There is an increasing number of specialist textbooks on bioinformatics, reflecting a growing student interest in the subject and pressure on universities to provide undergraduate and MSc courses in this area. Introduction to Bioinformatics is a first-rate response to these demands and provides lucid and well-written explanations of how and why to perform bioinformatic analyses. Arthur Lesk clearly explains the underlying logic of sequence analyses and illustrates what algorithms do, often by use of helpful analogies to everyday life.

Chapter one provides an introduction to, and overview of, bioinformatics, and itself would be useful for teaching the rudiments of the subject to first and second-year undergraduates. The remaining four chapters deal with genome organisation and evolution; archives and information retrieval; alignments and phylogenetic trees; and protein structure and drug design.

The physical production of the book is excellent, the text being well printed and the diagrams clear and easy to understand.

While Lesk concentrates on web-based software, he does encourage students to try writing simple programs in Perl, an easily available programming language. There are examples of Perl programs to draw helical protein wheels or DNA dotplots and exercises in writing Perl programs. Indeed, each chapter ends with a well-thought-out series of exercises and problems.

These would be useful for teaching a practical course in bioinformatics as there is a large number to choose from with a good variety of difficulty.

Lesk coins the term weblem for problems that require use of web resources, for example, performing sequence alignments on HOX clusters and using them to generate a phylogenetic tree. I particularly liked the weblem asking for a taxonomic classification of the organisms needed to make a full English breakfast.

Criticisms? Only a couple. A lecturer would find it helpful to have worked solutions to the problems. There is only brief mention of large-scale gene expression surveys by hybridisation to DNA micro-arrays. While there are fewer web resources dealing with micro-array data, it would be valuable to show how hybridisation data are processed and interpreted. The companion website is simply organised and its main value is as a collection of weblinks to the databases, programs and gateways referred to in the book.

Instant Notes in Bioinformatics is one in a series covering topics in biological sciences. The book consists of about 50 separate sections, of two to five pages, covering items such as data retrieval with Entrez, annotation tools and structure prediction by comparative modelling.

Despite the title, I am not sure what this book is for. The blurb on the back cover states that it is for "learning and rapid revision" and is suitable for undergraduates, postgraduates and researchers. However, I think it unlikely that many undergraduates would actually learn by reading it in isolation. There is certainly lots of information in the book but the explanations are often turgid and clunky, as highlighted by comparing treatment of the same topic with that provided in Introduction to Bioinformatics . When Lesk deals with building phylogenetic trees using clustering and cladistic approaches, methods are explained with clear diagrams of simple worked examples that break the process into basic components. By contrast, in Instant Notes the explanations are mainly given in text and coordinate poorly with the limited diagrams, making it harder to appreciate how the trees are built. There is a long glossary and a companion website consisting of a list of links to the websites presented in the book.

An Introduction to Computational Biochemistry is a more specialist book, as reflected in its price. The first half details theoretical explanations of topics such as reaction kinetics and structure determinations, as well as instructions on using computer software to handle and analyse biochemical data. The second half covers bioinformatic analyses of DNA and protein sequences.

The book is suited to third-year undergraduates and postgraduates. It is not an appealing book as much of it reads like an instruction manual, showing a screen view of a website and telling you which button to click. This is both tedious and a hostage to fortune as web interfaces are often updated.

Modern Genetic Analysis is the second edition of a book derived from a successful long-running text. It is aimed at first and second-year undergraduates and contains a wealth of information. As with many new genetics textbooks, the structure of genomes, the way genes work and transmission of DNA are presented before consideration of Mendelian inheritance.

Many of the changes to this edition are organisational: some elements have been moved and in other cases a chapter has been split into two or vice versa.

The chapter on genomics has been updated and there are new chapters on evolutionary genetics and mutational dissection. The latter topic is particularly welcome as it is often neglected. The logic of performing forward genetic screens is presented and there are explanations of mating schemes to identify mutants, and specialised tricks to screen for mutant phenotypes in model organisms.

There is a substantial companion website including practice tests and deconstructed problems supported by online grading. There are also animations of molecular processes and analytical techniques, also available on a CD-Rom that can be purchased with the book.

I was impressed by the web-based tutorials in bioinformatics that show students how to use databases and software offered by the National Center for Biotechnology Information. Explanatory information and instructions are in a strip in the browser window, leaving most of the screen free to view and use the interactive database itself. It is an attractive and productive way of showing students how they can gather and analyse information using web-based services.

Fred Tata is lecturer in genetics, University of Leicester.

Modern Genetic Analysis: Integrating Genes and Genomes

Author - Anthony J. F. Griffiths, William M. Gelbart, Richard C. Lewontin and Jeffrey H. Miller
ISBN - 0 7167 4382 5 and 4714 6
Publisher - Freeman
Price - £35.99 (£38.99 with CD-Rom)
Pages - 736

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