Beginning Perl for Bioinformatics

Chapter 9. Restriction Maps and Regular Expressions

In this chapter, I’ll give an overview of Perl regular expressions and Perl operators, two essential features of the language we’ve been using all along. We’ll also investigate the programming of a standard, fundamental molecular-biology technique: the discovery of a restriction map for a sequence. Restriction digests were one of the original ways to “fingerprint” DNA; this can now be simulated on the computer.

Restriction maps and their associated restriction digests are common calculations in the laboratory and are provided by several software packages. They are essential tools in the planning of cloning experiments; they can be used to insert a desired stretch of DNA into a cloning vector, for instance. Restriction maps also find application in sequencing projects, for instance in shotgun or directed sequencing.

Regular Expressions

We’ve been dealing with regular expressions for a while now. This section fills in some background and ties together the somewhat scattered discussions of regular expressions from earlier parts of the book.

Regular expressions are interesting, important, and rich in capabilities. Jeffrey Friedl’s book Mastering Regular Expressions (O’Reilly) is entirely devoted to them. Perl makes particularly good use of regular expressions, and the Perl documentation explains them well. Regular expressions are useful when programming with biological data such as sequence, or with GenBank, PDB, and BLAST files.

Regular ...