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.