d-Omix: a mixer of generic protein domain analysis tools

Abstract

Domain combination provides important clues to the roles of protein domains in protein function, interaction and evolution. We have developed a web server d-Omix (a Mixer of Protein Domain Analysis Tools) aiming 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 web server is freely available at http://www.biotec.or.th/isl/Domix.

An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins

“…Previously, there have been attempts to abstract the domain content and order of domain architectures and arrive at domain architecture distance scores and such comparisons can be performed at servers like PDART [11] and DAhunter [21], d-omix [22] etc. These are useful in comparing homologous architectures, whereas ADASS is a general purpose alignment-free algorithm for estimating similarity relationship between domain architectures irrespective of their homology relationships and is highly sensitive to distinguish proteins with unrelated domain architectures (Figure 5a).…”