The first screen in the web interface is the main search mechanism. In this page the user can query the database by entering an organism name and/or gene product name in the appropriate boxes. If the user does not enter an organism or gene product name, the program will return all entries in the database.
When the user submit a query a new page, containing all the entries that satisfy the search parameters, is open. This page displays information about each of the relevant entries and allow the user to select several genes for further analyses.
The following figure shows the results of a search for all Actin genes in the database (results page). The resulting table contains information about the genes in the database including: organism name, gene product, number of MDS, number of IES, is the gene scrambled, and the gi numbers of the GenBank files containing the MAC and MIC versions of the gene (these gi numbers are linked to the GenBank files, and if the user clicks on them they will open the GenBank file in a new window).
If the user clicks on a gene product name, a new page containing detailed information about the gene is opened in a new window. This new window contains: (A) the annotated MAC sequence of the gene with MDS in lowercase and pointers in uppercase, (B) the annotated MIC sequence of the gene with MDS and pointers in uppercase and IES in lowercase, and (C) a table with the MAC and MIC sequences of each MDS, the MAC sequence of the pointers and the IES sequences.
In the results page, the user also has the option to select various genes for a visual comparison by clicking in the boxes besides each gene. After selecting several genes, if the user clicks at the "Visually Compare the Sequences" button a page opens containing a figure that shows the scrambling pattern of all the selected genes.
In this new page the user can further refine the figure by selecting only a subset of the previously selected sequences and clicking on the "Compare Only the Selected Sequences" button. The figure show the locations of the MDS (red) and pointers (gree) in the MAC and MIC, and also the locations of the IES (blue) in the MIC, black lines connect the MIC and MAC versions of the MDS.
