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

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

ESTs in Plants: Where Are We Heading?

Expressed sequence tags (ESTs) are the most important resources for transcriptome exploration. Next-generation sequencing technologies have been generating gigabytes of genetic codes representing genes, partial and whole genomes most of which are EST datasets. Niche of EST in plants for breeding, regulation of gene expression through miRNA studies, and their application for adapting to climatic changes are discussed. Some of the recent tools for analysis of EST exclusive to plants are listed out. Systems biology though in its infancy in plants has influenced EST mapping for unraveling gene regulatory circuits, which is illustrated with a few significant examples. This review throws a glance at the evolving role of ESTs in plants