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The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction
Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Number of Authors: 32018 (English)In: Protein Science, ISSN 0961-8368, E-ISSN 1469-896X, Vol. 27, no 1, p. 195-201Article in journal (Refereed) Published
Abstract [en]

SubCons is a recently developed method that predicts the subcellular localization of a protein. It combines predictions from four predictors using a Random Forest classifier. Here, we present the user-friendly web-interface implementation of SubCons. Starting from a protein sequence, the server rapidly predicts the subcellular localizations of an individual protein. In addition, the server accepts the submission of sets of proteins either by uploading the files or programmatically by using command line WSDL API scripts. This makes SubCons ideal for proteome wide analyses allowing the user to scan a whole proteome in few days. From the web page, it is also possible to download precalculated predictions for several eukaryotic organisms. To evaluate the performance of SubCons we present a benchmark of LocTree3 and SubCons using two recent mass-spectrometry based datasets of mouse and drosophila proteins. The server is available at http://subcons.bioinfo.se/

Place, publisher, year, edition, pages
2018. Vol. 27, no 1, p. 195-201
Keywords [en]
subcellular localization, sequence analysis, machine learning
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:su:diva-152492DOI: 10.1002/pro.3297ISI: 000418254300019PubMedID: 28901589OAI: oai:DiVA.org:su-152492DiVA, id: diva2:1181103
Available from: 2018-02-07 Created: 2018-02-07 Last updated: 2018-02-07Bibliographically approved

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Salvatore, MarcoShu, NanjiangElofsson, Arne
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Science for Life Laboratory (SciLifeLab)Department of Biochemistry and Biophysics
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