Domain combination provides important clues to the roles of protein domains in protein function, interaction, and evolution. A web server d-Omix is a mixer of generic protein domain analysis tools aiming to serve as a unified platform to analyze, compare, and visualize protein data sets in various aspects of protein domain combinations. With InterProScan files for protein sets of interest provided by users, the server incorporates four services for domain analyses. First, it constructs protein phylogenetic tree based on a distance matrix calculated from protein domain architectures (DAs), allowing the comparison with a sequence-based tree. Second, it calculates and visualizes the versatility, abundance, and co-presence of protein domains via a domain graph. Third, it compares the similarity of proteins based on DA alignment. Fourth, it builds a putative protein network derived from domain-domain interactions from DOMINE. Users may select a variety of input data files and flexibly choose domain search tools (e.g., hmmpfam, superfamily) for a specific analysis. Results from the d-Omix could be interactively explored and exported into various formats such as SVG, JPG, BMP and CSV. Users with only protein sequences could prepare an InterProScan file using a service provided by the server as well.
The d-Omix was developed by BIOTEC's Information Systems Laboratory and is freely available at http://www.biotec.or.th/isl/Domix. This work has recently been accepted for publication in Nucleic Acids Research (NAR) (Impact factor: 6.954), 2009 Web Server Issue.
Posted on 30 April 2009.