• How can I visualize only membrane proteins (the membrane subproteome) ?
• How can I exclude membrane proteins from the visualization ?
• How can I visualize only the secretome or the membrane proteome ?
• How can I overlay an experimental 2D gel with a virtual one ?

The proteomes can either be imported from our database via the internet (computer icon in the toolbar) or by importing sequence information in FASTA or EMBL format ("File-->Load" menu). Don't forget to enable transmembrane helix prediction during the import progress. Depending on your machine this may take some minutes.

After importing the sequence data, choose "Tools-->Group Window" to open the group dialog. Select "allproteins" in the group selection box and uncheck the "show whole group" selection. When all proteins disappeared select the group "membrane proteome" and enable the "show whole group" checkbox. Now JVirGel is visualising only membrane proteins. By default a protein is considered as membrane protein if it consists of at least two predicted transmembrane helices. Of course, these settings can be altered.

There are two possibilities to exclude membrane proteins:

1. Open menu Tools->Membrane proteins, check "hide membrane proteins"
2. Open menu Tools->Group Window, choose group "membrane proteins" and uncheck "show whole group"

After importing the sequence data, choose Menu "Tools-->Group Window" to open the group dialog. Select "allproteins" in the group selection box and uncheck the "show whole group" selection. When all proteins disappeared select the group "membrane proteome" or "secretome" and enable the "show whole group" checkbox. Now JVirGel is visualising only membrane or secreted proteins. By default a protein is considered as membrane protein if it consists of at least two predicted transmembrane helices. Of course, these settings can be altered.

1. Import a genome. The simplest way is to click on the computer icon in the toolbar and import the genome from our database via the internet. You can also import proteomic data given in FASTA (amino acid sequences of course!!!) or EMBL format by clicking the open button in the toolbar. Don't forget to enable signal peptide prediction / correction.
2. Choose "identification" from the Menu "Tools" and the program awaits an experimental gel image. JVirGel is able to read png, gif, bmp and jpeg graphics. To avoid performance problems, the image width and height should not exceed 1500 pixel.
3. When your image is loaded you need to set some landmarks. This is done by choosing proteins with known positions in the list on the left hand side and than clicking on the corresponding gel positions. If you have set some landmarks (about 5 or more), you can enable the virtual gel by clicking on the virtual gel button on the toolbar (left).