JVirGel

JVirGel is a software for the simulation and analysis of proteomics data [1]. The JavaTM based software determines the theoretical isoelectric points (pI) and the calculated molecular weights (MW) of proteins and visualizes these as a virtual two-dimensional (2D) protein map. The user is able to control the presentation of the calculated 2D gel interactively by selecting a pI/MW range and an electrophoretic timescale of interest.

JVirGel exists in 3 different versions:

1. Standalone application:
   The application needs to be installed on the user's computer. However, the standalone application offers the most advanced features. Currently, the application is in beta stage and is available at the download section.
2. Java Applet:
   To run this version you need an installed Java Runtime Environment on your system. Due to the fact that the applet is transferred via the internet it is smaller than the standalone application. Thus the functional range of the applet is limited. Even though the applet offers the possibility to visualize 2D gels interactively. The applet can either import predefined data from the public database PRODORIC [2] or user-defined amino acid sequences in FASTA format. To start the applet click here.
3. HTML-Version:
   This is an alternative for those who do not have the possibility to run Java applets. The only condition to run this version is an installed webbrowser. However the functionality of this version is very limited. Click here to start this version of JVirGel and select HTML-version in the menu of the next page.

List of currently implemented features (standalone version):

• import of amino acid sequences from FASTA-, EMBL-file or from PRODORIC database via XML
• prediction and visualisation of secretomes
• predcition and visualisation of membrane proteomes
• translation of the Codon Adaptation Index (CAI) into protein spot size
• exclusion of membrane proteins from the visualisation
• accounting for signal peptides and in silico cleavage that results in a higher prediction accuracy of the pI and MW
• export of virtual gels to png- or jpg-graphics
• matching of an experimental gel with a virtual gel using different regression algorithms
• zooms into an user selectable pH/MW range
• proteins can be sorted into groups and all data can be exported in CSV-tables or MS-Excel spreadsheets
• proteins can be colored according to their content of transmembrane-helices or their probability to be secreted