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Beginning Perl for Bioinformatics by James Tisdall

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Bioperl

The Bioperl project is an important collection of Perl code for bioinformatics that has been in development since 1998. Although Bioperl uses the more advanced object-oriented style of Perl program design, it's possible to take an introductory look here at how it's organized and used.

The main focus of Bioperl modules is to perform sequence manipulation, provide access to various biology databases (both local and web-based), and parse the output of various programs.

Bioperl is available at http://www.bioperl.org/. Some of its features rely on having additional Perl modules—available from CPAN (http://www.cpan.org/)—installed. This situation is quite common, and as you do more Perl programming, you'll become familiar with installing modules from CPAN. The Bioperl tutorials include information on installing Bioperl and additional modules for the three major operating systems: Unix or Linux, Mac, and Windows.

Bioperl doesn't provide the programmer with complete programs. Rather, it provides a fairly large-and growing-set of modules for accomplishing common tasks, including some tasks you've seen in this book. You have to write the programs that use the modules. The goal of Bioperl is to make developing bioinformatics applications easier, by providing easy-to-use standard modules. There are example programs for most of the modules, which can be examined and modified to get started.

Like many open source projects, Bioperl has suffered from fragmentation and uneven documentation, ...

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