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d-Omix: a mixer of generic protein domain analysis tools
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Document Title
d-Omix: a mixer of generic protein domain analysis tools
Author
Wichadakul D, Numnark S, Ingsriswang S
Name from Authors Collection
Affiliations
National Science & Technology Development Agency - Thailand; National Center Genetic Engineering & Biotechnology (BIOTEC)
Type
Article
Source Title
NUCLEIC ACIDS RESEARCH
ISSN
0305-1048
Year
2009
Volume
37
Open Access
Green Submitted, Green Published, gold
Publisher
OXFORD UNIV PRESS
DOI
10.1093/nar/gkp329
Format
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.
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
Funding Sponsor
Cluster Program Management Office (CPMO) [FC0033 B21, SPA B1-1]; National Science and Technology Development Agency ( NSTDA), Thailand; Cluster Program Management Office [FC0033 B21]
License
CC BY-NC
Rights
Authors
Publication Source
WOS