There are three possibilities to import proteome sequence data into JVirGel:

1. Import Data in XML format over the Internet

  1. The simplest way to import proteomic data is the XML-Import function of JVirGel. Just click on the computer icon in the toolbar to open the XML-Import dialog:

    import
  2. Select an organism. If you want JVirGel to predict the Sec-dependent secretome or the membrane subproteome enable signal peptide prediction and respectively transmembrane helices prediction by checking the corresponding checkboxes.

    import dialog
    Note: The prediction of transmembrane helices may take some minutes depending on your hardware and the selected organism.
  3. To start the XML-import just click the Start button. Be sure, that your firewall allows JVirGel to connect the database.

    JVirGel
  4. Congratulations, you have just created your first virtual gel !



2. Import Sequence Data in FASTA Format

  1. In order to import your own sequence files in FASTA format, click on the Open icon in the toolbar. After selecting your FASTA-file the FASTA-import dialog appears:

    Toolbar Fasta
  2. If you want JVirGel to predict the Sec-dependent secretome or the membrane subproteome enable signal peptide prediction and respectively transmembrane helices prediction by checking the corresponding checkboxes.

    FASTA-Import Dialog
    Note: The prediction of transmembrane helices may take some minutes depending on your hardware and the number of imported proteins.
  3. Congratulations, you have just created your first virtual gel !

    JVirGel


3. Import Sequence Data in EMBL Format

Note:
  1. In order to import your own sequence files in EMBL format, click on the Open icon at the toolbar. After selecting an EMBL file the EMBL-import dialog appears:

    Toolbar EMBL
  2. If you want JVirGel to predict the Sec-dependent secretome or the membrane subproteome enable signal peptide prediction and respectively transmembrane helices prediction by checking the corresponding checkboxes. Furthermore, JVirGel is able to predict Codon Adaptation Indices (CAI) if you check the appropriate checkbox.

    EMBL-Import Dialog
    Note: The prediction of transmembrane helices may take some minutes depending on your hardware and the number of imported proteins.
  3. Congratulations, you have just created your first virtual gel !

    JVirGel