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Mastering Perl for Bioinformatics is the follow-up to Tisdall’s earlier Beginning Perl for Bioinformatics. Both books are part of O’Reilly’s lauded “animal books” series; Beginning was graced with tadpoles, while Mastering sports a frog.

Naturally, the book picks up where the earlier one left off, diving headfirst into the details of Perl modules. Chapter two is a quick pass over some basic data structures, with discussion of how you’d implement each in Perl. Subsequent chapters cover object-oriented programming in Perl, using Perl with relational databases, using Perl with web services, generating graphics on the fly with Perl, and the use of the Bioperl (http://www.bioperl.org) suite of libraries.

As might be expected, all the coding examples in the book are drawn from reasonably realistic bioinformatics situations. There’s a little bit less hand-holding on the biological side in this book, relative to the earlier volume — which I think is a good idea, as it gives more space to focus on the programming material.

The one weakness of this book is that it covers quite a few topics, which means that it doesn’t really go into great depth on any of them. The “survey” approach is well done, and it’s very nice to have biologically relevant examples and exercises for the breath of material that is addressed, but I think the book might have been stronger if it forewent the “Perl and the Web” and “Perl and Graphics” chapters in favor of more focus on the Bioperl libraries.

If you’re a bioinformatics programmer who enjoyed Beginning Perl for Bioinformatics, and you want to get a better idea of what more advanced Perl programming looks like and what sorts of things you can do with Perl, this book is a nice place to start. However, if you’re looking for more specific information, other more focused books might be a better choice, if you can live without the biologically focused code examples.

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