GCG: Drawing Linear Restriction Maps

Abstract

To produce a restriction map using a computer program a single sequence (your target sequence) is matched against a predefined sequence pattern database (referred to as “enzymes”). The pattern database used must obey some rules with respect to the pattern definition language, and what an individual pattern means. The pattern matching algorithm should be flexible enough to allow modifications to its stringency. With respect to enzyme cleavage, this is fairly easy to achieve in nucleotide sequences, as described in this chapter. It becomes more difficult when dealing with protein sequences (see Chapter 12 and Chapters 12 and 13 in Part II). Pattern matching methods are important in many other fields and are not necessarily restricted to enzyme cleavage (see Chapter 10 and Chapters 8 and 9 in Part II).