Nucleic Acids Research Advance Access originally published online on May 21, 2009
Nucleic Acids Research 2009 37(Web Server issue):W417-W421; doi:10.1093/nar/gkp329
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W417-W421
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
d-Omix: a mixer of generic protein domain analysis tools
National Center for Genetic Engineering and Biotechnology (BIOTEC) - Information Systems Laboratory (ISL), Pathumthani, Thailand
*To whom correspondence should be addressed. Tel: +66 0 2564 7000, ext. 5536; Fax: +66 0 2564 6607; Email: duangdao.wic{at}biotec.or.th
Received February 20, 2009. Revised April 17, 2009. Accepted April 20, 2009.
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.