JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins.
BACKGROUND
After the publication of JVirGel 1.0 in 2003 we got many requests and suggestions from the proteomics community to further improve the performance of the software and to add additional useful new features.


RESULTS
The integration of the PrediSi algorithm for the prediction of signal peptides for the Sec-dependent protein export into JVirGel 2.0 allows the exclusion of most exported preproteins from calculated proteomic maps and provides the basis for the calculation of Sec-based secretomes. A tool for the identification of transmembrane helices carrying proteins (JCaMelix) and the prediction of the corresponding membrane proteome was added. Finally, in order to directly compare experimental and calculated proteome data, a function to overlay and evaluate predicted and experimental two-dimensional gels was included.


BACKGROUND
JVirGel 2.0 is freely available as precompiled package for the installation on Windows or Linux operating systems. Furthermore, there is a completely platform-independent Java version available for download. Additionally, we provide a Java Server Pages based version of JVirGel 2.0 which can be operated in nearly all web browsers. All versions are accessible at http://www.jvirgel.de
Hiller
Karsten
K
Institut für Mikrobiologie, Technische Universität, Braunschweig Spielmannstrasse 7, D-38106 Braunschweig, Germany.
Grote
Andreas
A
Maneck
Matthias
M
Münch
Richard
R
Jahn
Dieter
D
D000465:Algorithms; D000595:Amino Acid Sequence; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D008565:Membrane Proteins / Q000032:analysis / Q000737:chemistry*; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods*; D021382:Protein Sorting Signals; D020543:Proteome / Q000032:analysis / Q000737:chemistry* / Q000378:metabolism*; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D008565:Membrane Proteins; D021382:Protein Sorting Signals; D020543:Proteome