The Map View is a chromosome-based display.
– Useful for locating where your gene or SNP lies in a species’ chromosomes.
– Allows for quick exporting of PNG files for use in publications (see: “Exporting as a PNG” below)
The visuals: explained
– To the right of the chromosome are all the genes which are related to the search term(s). Coloured horizontal lines distinguish genes, with green for high scores, orange for medium, and red for low.
– SNPs are shown to the left as the highlighted squares, colour coded according to the study shown in the SNP legend, relating to evidence found for the SNP.
Visible Centromeres
Centromere positions are shown as grey horizontal lines.
– They are only visible in species containing the data and where the search resulted in genes being shown on the chromosome band of interest (no centromeric positions will show if there are no genes on the band).
– The position data is added manually from journal articles where available. Where unavailable we sometimes use bioinformatic methods to infer their positions as accurately as possible. They are meant to be used as a general visual guide but will not always be available.
Creating a Network
Select one or more genes (from the right of individual chromosomes) and click the “Create Network” button at the bottom right of the Map View interface.
Map view with Genome Region Search
You can also specify a region search and only show genes and SNPs within this region.
Exporting as a PNG
Clicking the download icon in the top right of the interface bar allows for quickly downloading the Map View interface as a PNG.
Note that what is currently on screen is what will be saved.
Controls and settings
You can zoom in and out and side to side interactively using mousewheel and left mouse button to click+drag. Right clicking SNPs will provide further information in a pop-up box, where the selected SNP/QTL can be hidden or displayed.
