REVIEW - Beginning Perl for Bioinformatics


Beginning Perl for Bioinformatics


James Tisdall




O'Reilly (2001)




Robert W. Hand


October 2002



This book is a curious, hybrid that teaches the computer language Perl, on one hand and serves as an introduction to the rapidly growing field of Bioinformatics, on the other. The author recommends the book as a 'practical introduction to programming for biologists'. Since our organisation is for C and C++ programmers rather than for biologists, this book and my review might seem 'off-topic'. However, I found the book to be excellent and the author pulls off the marriage of his two aims quite well.

The first three chapters contain very basic information for the novice programmer - how to get and install Perl, how to get a text editor, how to back up work. The advice is sound, but an experienced programmer could skim them without loss of direction.

At this point, I started to read Appendix B, Perl Summary. This appendix reads very well, provides a good reference to the language and is worth the price of the book. In particular, the pace of the presentation is consistent with the reading appetite of an experienced programmer. The section on regular expressions is especially noteworthy.

Chapters four through nine contain the meat of the book. The focus is on writing programs to analyse DNA, genes and proteins. As a result, some Perl topics are omitted and others are emphasised. For example, the important use of Perl in cgi programming is mentioned only in passing. The example programs do illustrate important programming principles while allowing illustrations of the power of Perl in the field of Bioinformatics. The approach is practical rather than theoretical. The requisite biology is explained in very simple and abstracted terms that should be understandable by the non-biologist.

Chapters ten through twelve introduce the GenBank, Protein Data Bank, and BLAST with good examples of Perl programs that manipulate such data. Unfortunately, the biological detail started to strain my knowledge of molecular biology.

This book was my first encounter with Perl. I found that I could read it quickly and there appear to be few errors. I recommend it to readers who are interested in the application of Perl to Bioinformatics.ADO, COM etc.

Book cover image courtesy of Open Library.