HMM Search for Apoptotic Domains (MOLECULAR BIOLOGY AND INFORMATION-Biological Information Science)

Abstract

For the purpose of analyzing apoptotic molecular interactions, we have developed a knowledge base, which consists of apoptotic molecular interactions, together with the WWW interface for it. This database and the user interface enabled us to find out entries containing various information about cell death. This information tells us that the apoptotic molecular interactions are likely to be controlled under a series of specific conserved domains. Thus, the viewpoint of domain seems to be more effective than the sequence similarity of the entire protein, when analyzing pathways, molecules, genes and genomes. In this study, we collected several hundred domain sequences of apoptotic interactions from our database, made 14 Hidden Markov Models (HMMs) for the domain groups, and searched against KEGG/GENES database with those HMMs to detect evolutionarily conserved domains.