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Bioinformatics Advance Access published online on July 26, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl409
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received April 18, 2006
Revised July 14, 2006
Accepted July 22, 2006

Applications note

JVirGel 2.0: computational prediction of proteomes separated via two dimensional gel electrophoresis under consideration of membrane and secreted proteins

Karsten Hiller 1, Andreas Grote 2, Matthias Maneck 3, Richard Münch 1, and Dieter Jahn 1 *

1 Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
2 Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany; Institut für Bioverfahrenstechnik, Technische Universität Braunschweig, Gaußstr. 17, D-38106 Braunschweig, Germany
3 Fachbereich Mathematik und Informatik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany

* To whom correspondence should be addressed.
Dieter Jahn, E-mail: d.jahn{at}tu-bs.de


  Abstract

Motivation: 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 proteomedata, a function to overlay and evaluate predicted and experimental two dimensional gels was included.

Availability: 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 webbrowsers. All versions are accessible at http://www.jvirgel.de.

Associate Editor: Dmitrij Frishman
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