{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:26:46Z","timestamp":1767961606543,"version":"3.49.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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 web browsers. All versions are accessible at .<\/jats:p>\n               <jats:p>Contact: \u00a0d.jahn@tu-bs.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl409","type":"journal-article","created":{"date-parts":[[2006,7,27]],"date-time":"2006-07-27T00:58:50Z","timestamp":1153961930000},"page":"2441-2443","source":"Crossref","is-referenced-by-count":32,"title":["JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins"],"prefix":"10.1093","volume":"22","author":[{"given":"Karsten","family":"Hiller","sequence":"first","affiliation":[{"name":"Institut f\u00fcr Mikrobiologie, Technische Universit\u00e4t Braunschweig 1 \u00a0 1 \u00a0 \u00a0 Spielmannstrasse 7, D-38106 Braunschweig, Germany"}]},{"given":"Andreas","family":"Grote","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Mikrobiologie, Technische Universit\u00e4t Braunschweig 1 \u00a0 1 \u00a0 \u00a0 Spielmannstrasse 7, D-38106 Braunschweig, Germany"},{"name":"Institut f\u00fcr Bioverfahrenstechnik, Technische Universit\u00e4t Braunschweig, Gau\u00dfstrasse 17, D-38106 Braunschweig 2 \u00a0 2 \u00a0 \u00a0 Germany"}]},{"given":"Matthias","family":"Maneck","sequence":"additional","affiliation":[{"name":"Fachbereich Mathematik und Informatik, Freie Universit\u00e4t Berlin, Arnimallee 14, D-14195 Berlin 3 \u00a0 3 \u00a0 \u00a0 Germany"}]},{"given":"Richard","family":"M\u00fcnch","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Mikrobiologie, Technische Universit\u00e4t Braunschweig 1 \u00a0 1 \u00a0 \u00a0 Spielmannstrasse 7, D-38106 Braunschweig, Germany"}]},{"given":"Dieter","family":"Jahn","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Mikrobiologie, Technische Universit\u00e4t Braunschweig 1 \u00a0 1 \u00a0 \u00a0 Spielmannstrasse 7, D-38106 Braunschweig, Germany"}]}],"member":"286","published-online":{"date-parts":[[2006,7,26]]},"reference":[{"key":"2023012409242845800_b1","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1002\/pmic.200300396","article-title":"ProteomeWeb: a web-based interface for the display and interrogation of proteomes","volume":"3","author":"Babnigg","year":"2003","journal-title":"Proteomics"},{"key":"2023012409242845800_b2","doi-asserted-by":"crossref","first-page":"D582","DOI":"10.1093\/nar\/gkh089","article-title":"GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes","volume":"32","author":"Babnigg","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012409242845800_b3","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1093\/protein\/10.6.673","article-title":"Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method","volume":"10","author":"Cserz\u00f6","year":"1997","journal-title":"Protein Eng."},{"key":"2023012409242845800_b4","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological Sequence Analysis Probabilistic Models of Proteins and Nucleic Acids","author":"Durbin","year":"1998"},{"key":"2023012409242845800_b5","doi-asserted-by":"crossref","first-page":"7357","DOI":"10.1128\/MCB.19.11.7357","article-title":"A sampling of the yeast proteome","volume":"19","author":"Futcher","year":"1999","journal-title":"Mol. 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