Figure 1

The interface of MGcV. The interface comprises seven separate modules. 1) Input: Copy/paste the input containing regions of interest and select the appropriate input-type. The context is visualized by clicking “Visualize context”. Input-types include lists of identifiers such NCBI GI-codes or NCBI locus tags, genomic regions, or phylogenetic trees in newick format. Identifiers can also be searched for using the buttons “Identifier” and “BLAST”. 2) In the map settings, the appearance of the comparative context map can be altered. Various settings can be changed, which include the scale, the orientation, the gene-label and the data on display (e.g. COG coloring, PFAM, protein location). To apply the changes the “Adjust settings”-button has to be clicked. 3) Data can be added via data import. Users can upload the position of genomic elements (e.g. regulatory elements) and gene-associated quantitative data (e.g. microarray data). Subsequently, the user can include the data in the map or generate a (ranked) comparative context map based on the uploaded data (blue arrows). 4) Sequence and functional data like upstream regions, gene sequences, cog categories, annotations can be obtained for visually selected genes via data export. Genes can be included or excluded by clicking. 5) The functional data related to a particular gene context is displayed in a single lane in the comparative genome map, thereby allowing for a direct comparison of the data between various strains or species. The maps are interactive; hovering the mouse over the map will display additional information (e.g. NCBI GI, gene product, COG) and clicking genes will tag them for data export. 6) The map can be converted to PNG- or PDF- format. 7) The interface is linked to a tutorial, to a color legend, to the circular viewer of the original MGV, and also directly to the MEME website.