Using VariVis
Once VariVis has been installed, you can use VariVis simply by linking from within your databases user interface to either of gel.cgi or varivis.cgi.
varivis.cgi
varivis.cgi will first present the user with an overview of the entire gene structure at the top of the screen. Clicking on this overview will display below it a horizontal representation of that gene segment with the sequence, variations and structural features displayed. Users will then be able to zoom in or out, click on variants to access more information, or change their field of view.
gel.cgi
gel.cgi has the same functionality as varivis.cgi but has a vertical representation of the gene sequence in the unique "Gel" view.
Both these files contain links to each other, allowing the user to change their style of viewing to suit their individual preferences. These files also contain a link to sequence.cgi to allow the user to view and easily copy the raw reference sequence.
Linking to a specific area
VariVis uses the URI encoded upper and lower variables to specify the sequence position it displays. You can direct VariVis to display a specific section of a gene by constructing a custom link to either the gel.cgi or varivis.cgi script.
For example, to display only the 100bp segment of the gene, from position 101 to 200, you can use the link gel.cgi?lower=101&upper=200. Please note: the values these variables take are the absolute, or genomic, coordinates, with 1 being the first nucleotide in the sequence. Coding sequence coordinates (e.g. -12,80+1,*2) will not function.
To link to a specific variant, you can make use of the URI encoded variable var. This variable takes a single variant name (in HGVS format) as an argument. URIs with this variable will cause VariVis to display the variant with a 10bp segment of the flanking sequence on each side.