Hiller Karsten, Grote Andreas, Maneck Matthias, Münch Richard, Jahn Dieter
Institut für Mikrobiologie, Technische Universität, Braunschweig Spielmannstrasse 7, D-38106 Braunschweig, Germany.
Bioinformatics. 2006 Oct 1;22(19):2441-3. doi: 10.1093/bioinformatics/btl409. Epub 2006 Jul 26.
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.
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.
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
2003年JVirGel 1.0发布后，我们收到了蛋白质组学领域的许多请求和建议，希望进一步提高该软件的性能并添加更多有用的新功能。
将用于预测依赖Sec的蛋白质输出信号肽的PrediSi算法集成到JVirGel 2.0中，可以从计算出的蛋白质组图谱中排除大多数输出的前体蛋白，并为基于Sec的分泌蛋白组计算提供基础。添加了一个用于识别携带跨膜螺旋的蛋白质的工具（JCaMelix）以及相应膜蛋白质组的预测功能。最后，为了直接比较实验和计算的蛋白质组数据，加入了一个用于叠加和评估预测的二维凝胶与实验二维凝胶的功能。
JVirGel 2.0作为预编译包可免费获得，用于在Windows或Linux操作系统上安装。此外，还有一个完全独立于平台的Java版本可供下载。此外，我们提供了一个基于Java Server Pages的JVirGel 2.0版本，几乎可以在所有网页浏览器中运行。所有版本均可在http://www.jvirgel.de上获取
