title: JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins.
abstract: 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
authors.affiliation: Institut für Mikrobiologie, Technische Universität, Braunschweig Spielmannstrasse 7, D-38106 Braunschweig, Germany.
authors.forename: Karsten
authors.initials: K
authors.lastname: Hiller
authors.forename: Andreas
authors.initials: A
authors.lastname: Grote
authors.forename: Matthias
authors.initials: M
authors.lastname: Maneck
authors.forename: Richard
authors.initials: R
authors.lastname: Münch
authors.forename: Dieter
authors.initials: D
authors.lastname: Jahn
mesh_terms: 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
chemical_list: D008565:Membrane Proteins; D021382:Protein Sorting Signals; D020543:Proteome