ELISA: A Unified, Multidimensional View of the Protein Domain Universe

Boris E. Shakhnovich (borya@bu.edu)
John Max Harvey (max10@bu.edu)
Charles DeLisi (delisi@bu.edu)

Bioinformatics Program, Boston University, 44 Cummigton St., Boston MA 02215, USA


Abstract

ELISA (http://romi.bu.edu/elisa/) is a database that was designed for flexibility in defining interesting queries about protein domain evolution. We have defined and included both the inherent characteristics of the domains such as structure and function and comparisons of these characteristics between domains. Thus, the database is useful in defining structural and functional links between related protein domains and by extension sequences that encode them. In this database we introduce and employ a novel method of functional annotation and comparison. For each protein domain we create a probabilistic functional annotation tree using GO. We have designed an algorithm that accurately compares these trees and thus provides a measure of “functional distance” between two protein domains. Along with functional annotation, we have also included structural comparison between protein domains and best sequence comparisons to all known genomes. The latter enables researchers to dynamically do searches for domains sharing similar phylogenetic profiles. This combination of data and tools enables the researcher to design complex queries to carry out research in the areas of protein domain evolution, structure prediction and functional annotation of novel sequences.

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Japanese Society for Bioinformatics