Bioinformatical Methods for Domain Detection

Over the years there have been considerable improvements in the available sequence analysis techniques. In particular the sequence profile method [3] with its more recent extension to generalized profiles [4], and various fJidden Mar- 

The aforementioned properties make profile and HMM methods well suited for domain-detection purposes [8]. A large number of homology domains have been identified by each method, including several of the functional domains discussed below. 

When a novel homology domain has been discovered, it is possible to store the corresponding domain descriptor (profile or HMM) in a number of dedicated domain databases, which can be used to analyze newly identified sequences for their domain content [9, 10]. Several competing domain- and motif-databases exist, including PROSITE, PFAM, SMART, and Superfam, which contain descriptors for most, if not all, of the known domains involved in the ubiquitin system [11-14]. Recently, a new meta-database named INTERPRO has been established, which tries to combine the descriptors of several domain databases under a single user interface [15]. Pointers to the very useful search engines of the domain databases are provided in Table 12.1. 

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