Section: Application Domains

Bioinformatics

We consider protein functional sites. Functional sites and signatures of proteins are very useful for analyzing raw biological data or for correlating different kinds of existing biological data. These methods are applied, for example, to the identification and characterization of the potential functions of new sequenced proteins. The sites and signatures of proteins can be expressed by using the syntax defined by the PROSITE databank, and written as a “protein regular expression”. Searching one such site in a sequence can be done with the criterion of the identity between the searched and the found patterns. Most of the time, this kind of analysis is quite fast. However, in order to identify non perfectly matching but biologically relevant sites, the user can accept a certain level of error between the searched and the matching patterns. Such an analysis can be very resource consuming.