Perl is an ideal language for such needs. With Perl one will sometimes be able to solve a data search or manipulation problem in a matter of hours if not minutes. (Solving the same problem in C/C++/Java could take much, much longer.) Here are some particular problems in this setting for which Perl is a great fit.

 Searching sequence databases with regular expression patterns.

 Parsing entries in databases (e.g., reading a Genbank entry of a gene and extracting its exons).

 Converting database entries from one format to another (e.g., converting from Genbank to EMBL format).

 Using standard sequence analysis tools written in Perl. (See the various Perl packages supported by the BioPerl project.)

This short book introduces Perl to the bio or computer scientist interested in or working in bioinformatics. Chapter 1 covers data types. Chapter 2 covers control structures. Chapter 3 covers input and output. Chapter 4 covers regular expressions. Chapter 5 covers handy functions on strings. Chapter 6 covers subroutines. All these chapters contain illustrative examples from bioinformatics. These chapters cover only those features of Perl that are particularly important to know in the context of search and manipulation of biomolecular data. In particular, Unix-specific features such as those involving Unix file, directory and process management are omitted. Chapter 7 presents several Perl scripts for various common bioinformatics tasks. Chapter 8 covers the BioPerl project.