Figure 6

ArabiTag linking to Integrated Genome Browser. Screen captures showing query and results pages from ArabiTag http://www.transvar.org/arabitag are shown. A page describing alternative splicing of AT2G39730 (encoding rubisco activase) offers an "IGB link" icon that, when clicked, directs the currently running instance of the Integrated Genome Browser to display the region specified in the IGB link. For convenience, the page also includes a link to the on-line launch page for the IGB software http://www.bioviz.org/igb. To use the IGB link, users download and launch a copy of the IGB software, load the spliced EST and TAIR9 mRNA data sets from the BioViz DAS2 and BioViz Quickload data sources, setting the load mode for the TAIR9 mRNA data set to "Whole Genome." Clicking the IGB link within the ArabiTag Web page directs IGB to zoom and scroll to the Difference Region for this AS choice. Clicking the "Refresh Data" button instructs IGB to retrieve all the spliced ESTs that overlap the region, allowing the user to compare their boundaries with the TAIR9 gene models. Clicking an EST (as shown in the image) activates an edge-matching function, where all items with boundaries identical to the selected item (an EST in this case) acquire an edge-matching icon - a white bar drawn on top of the matching boundary. Right- (or control-clicking) the EST offers the user the option to visit the NCBI Web site and view the dbEST record for the selected EST, revealing it comes from a library prepared from salt-stressed seedlings.