1. Import Data in XML format over the Internet
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:
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.
Note: The prediction of transmembrane helices may take some minutes depending on your hardware and the selected organism.To start the XML-import just click the Start button. Be sure, that your firewall allows JVirGel to connect the database.
Congratulations, you have just created your first virtual gel !
2. Import Sequence Data in FASTA Format
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:
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.
Note: The prediction of transmembrane helices may take some minutes depending on your hardware and the number of imported proteins.Congratulations, you have just created your first virtual gel !
3. Import Sequence Data in EMBL Format
- We highly recommend to use EMBL Genome Reviews with JVirGel. You can download these files from the EBI webserver.
- The downloaded files need to be unzipped and renamed to "*.embl".
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:
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.
Note: The prediction of transmembrane helices may take some minutes depending on your hardware and the number of imported proteins.Congratulations, you have just created your first virtual gel !