What are patterns?

Many important sequence features, such as binding sites or the active sites of enzymes, consist of only a few amino acids that are essential for protein function. Patterns are very good at recognising such features. They are built by identifying these regions in multiple sequence alignments. The pattern of conservation within the sequence feature is then modelled as a regular expression, as is indicated in Figure 13.

Information

Learn more about regular expressions here

 

Figure 13. When creating patterns, a conserved motif is used to build a regular expression. The pattern illustrated here is translated as: [Ala or Cys]-any-Val-any-any-any-any-{any but Glu or Asp}.

Figure 13 When creating patterns, a conserved motif is used to build a regular expression. The pattern illustrated here is translated as: [Ala or Cys]-any-Val-any-any-any-any-{any but Glu or Asp}.

 

An example of a database that uses patterns is PROSITE (Bairoch, A. 1991).