To begin exploring - navigate to the search page through the "Search" link near the top of this page. You are presented with a dialog box on the left hand side and example queries on the right hand side of the page.

To begin, copy all of the rice gene identifiers from the example box and paste them to the dialog box on the left hand side, there are 4 gene identifiers. Note that the example identifiers are a mix of TIGR and RAP identifiers; you can paste any mix of these identifiers in and the system will recognize them and report accordingly. Click on the "Query" button, which navigates you to the result page.

The result page shows you one result per gene for every gene you queried on the previous page. Since the examples only contain four genes, you should now see four resulting rows. Each row shows you several parts of information: The first part is the header (beginning with a '>' symbol), and contains two lines of information identifying the gene on the first line and its chromosomal co-ordinates on the second; the second part is a list of motifs that have been mapped to the gene's promoter.

By clicking on the first line of the header for any gene, the browser will navigate to the RAP database and display GBrowse information in a separate window. Clicking on the second line will open and present relevant information for the gene, its promoter and the locations and scores of motifs mapped to the gene's promoter. Similarly, each motif in the results page may also be clicked. Doing so will yield information on the position weight matrix and consensus sequence for that motif.


South African National Bioinformatics Institute
© 2018