A typical display of a maize GSS contig record at PlantGDB. The lower left diagram displays a schematic representation of a GSS contig and its gene structure. In this example, the GSS contig appears to encode a full-length maize ABC transporter (based upon spliced alignment with three similar Arabidopsis gene products). Predicted exons are shown as solid lines, and introns are represented by thin lines. Known repetitive elements are masked and appear along the contig as yellow Xs. This diagram can be manipulated using the “Image Control” box located in the upper left. Researchers can add, e.g. EST spliced alignments, to the display by checking the appropriate box within the “Image Control” diagram then clicking the button labeled “Redraw Image.” In the middle, the “Similar protein sequences” scrollable box displays descriptions of matched proteins. On the right, the “Utilities” box contains a set of analysis tools that can be applied to the contig. For example, researchers can choose to view the details of the spliced alignments, perform a BLAST search against chosen databases, see detailed descriptions of matched proteins, etc. Near the bottom, a “Help” message box explains the function of each analysis tool as the researcher moves the computer mouse across the tool links. Researchers can provide expert annotation for the gene by following the link to “Provide Annotation” near the bottom of the “Utilities” box.

The PlantGDB TableMaker query tool. This display shows an example of constructing and executing a simple query to “Find all maize promoter sequences” (translated as “promoter organism equals Zea mays”). Once the fields that should be displayed in the output have been specified (middle panel of the same display), the researcher presses the button to execute the query. The output list (lower left) shows all sequences that match the query. Pressing the button to “Get all displayed features” downloads the features in FASTA format (bottom right). All query fields are based on GenBank annotation features. Detailed help and a tutorial resource are available from the TableMaker Web page.