Odd as it may seem at first, a book combining the basics of molecular biology and a programming language popular among system administrators and Web programmers can shed considerable light on one of the most active areas of interdisciplinary research in computer science and biology. This book does precisely that. It presents a concise and very readable introduction to the area of bioinformatics, supported by comprehensive examples of applied computational techniques implemented in the Perl programming language. This achievement looks even more remarkable if one considers that neither knowledge of computational molecular biology, nor familiarity with Perl, is assumed as a prerequisite.

The book seeks to meet the needs of readers with a computer science background, as well as those of readers approaching the issue from a biological sciences perspective. This is, I believe, its main strength. Viewed from this angle, the choice of Perl, with all its idiosyncrasies, isn’t really odd at all. Perl allows the techniques and algorithms explained in the book to be described briefly and clearly, thanks to its flexible syntax and comprehensive built-in support for string, list, and array manipulation, as well as its garbage collection mechanism, which frees programmers from having to deal with memory allocation details.

All chapters follow a regular presentation pattern, to which the reader soon becomes accustomed. The author starts with an introduction to the molecular biology background of a bioinformatics issue, and then progressively casts it in a computational language, culminating with a Perl implementation. The presentation of the theoretical background is usually short enough that computer science readers do not lose interest by becoming entangled in a web of unknown concepts, and long enough, in that it stimulates their curiosity. In the end, the algorithms help the computationally minded reader see coherence among the various biological concepts introduced. Readers with biological sciences backgrounds will probably find themselves in a nicely symmetrical situation, in which their better grasp of the introductory material helps them understand the algorithmic aspects of the problem.

As far as Perl programming is concerned, the book follows a natural progression. Programming concepts and Perl syntax are introduced as demanded by the bioinformatics applications described in the successive chapters. On the other hand, apart from the material covered in the initial chapters, the biological sciences content is more loosely connected. The book starts with an exposition of the basic concepts in genetics (its “central dogma”) in terms of DNA, RNA, proteins, and chromosomes, and illustrates its computational aspects (the processes of transcription and translation) with a simple program. The text then covers the complex problem of RNA secondary structure prediction, introducing dynamic programming techniques that reoccur in one form or another in later chapters. These are followed by an extensive (though not exhaustive) coverage of problems of both theoretical and practical interest in computational molecular biology. The former include sequence alignment, phylogeny reconstruction, coding sequence prediction and gene finding, and protein function identification by motif, as well as homologous sequence search, sequence assembly, and other computationally-challenging problems. The latter include database formats and search heuristics, such as FASTA and BLAST, dynamic programming methods, substitution matrices, and various optimization methods. At this point, one must have realized that the above issues are based on mathematics. All chapters are largely self-contained, incorporating brief explanations of the required probability, information theory, and computational complexity theory backgrounds. In order to truly appreciate the nature and limitations of the techniques described in the book, however, the reader needs more familiarity with those areas than a 320-page volume can offer.

The book lacks a discussion of future research directions, and does not provide pointers to the relevant literature to complement the basic bibliographic notes provided at the end of each chapter. Since the author excited the reader’s curiosity and described a possible (but often very basic) solution to a problem, I expected to get at least a glimpse of the state-of-the-art. This is a minor point, however. By and large, I found this to be an excellent book, and would not hesitate to recommend it to advanced undergraduate and postgraduate students.