Detection of Apoptotic Domains Against KEGG Database by the HMM Search

Abstract

We have developed the knowledge base which consists of apoptotic molecular interactions [1], and provided the WWW interface for it. This database and user interfaces enabled us to find out entries containing different information about cell death. This information tells us that the apoptotic molecular interactions are supposed to be controlled under a series of specific conserved domains, like Bcl-2 homology domain, death domain or death effector domain. So the viewpoint of domain seems to be more effective, rather than the entire sequence, when analyzing pathways, molecules, genes and genomes, which are concerned with apoptosis. In this study, we collected a few hundred domain sequences of apoptotic interactions from our database, made 14 hidden Markov models for the domain groups, and searched against KEGG/GENES database [2] with those HMMs (hidden Markov models) to detect conserved domains.