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Cell-PLoc 2.0: an improved package of web-servers for predicting subcellular localization of proteins in various organisms

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DOI: 10.4236/ns.2010.210136    7,119 Downloads   14,647 Views Citations

ABSTRACT

Cell-PLoc 2.0 is a package of web-servers evolved from Cell-PLoc (Chou, K.C. & Shen, H.B., Nature Protocols, 2008, 2:153-162) by a top-down approach to improve the power for predicting subcellular localization of proteins in various organisms. It contains six predictors: Euk-mPLoc 2.0, Hum-mPLoc 2.0, Plant-mPLoc, Gpos-mPLoc, Gneg-mPLoc, and Virus-mPLoc, specialized for eukaryotic, human, plant, Gram- positive bacterial, Gram-negative bacterial, and virus proteins, respectively. Compared with Cell-PLoc, the predictors in the Cell-PLoc 2.0 have the following advantageous features: (1) they all have the capacity to deal with the multiplex proteins that can simultaneiously exist, or move between, two or more subcellular location sites; (2) no accession number is needed for the input of a query protein even if using the “high- level” GO (gene ontology) prediction engine; (3) the functional domain information and sequential evolution information are fused into the “ab initio” sequence-based prediction engine to enhance its accuracy. In this protocol, a step- to-step guide is provided for how to use the web server predictors in the Cell-PLoc 2.0 package, which is freely accessible to the public at http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc-2/.

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Chou, K. and Shen, H. (2010) Cell-PLoc 2.0: an improved package of web-servers for predicting subcellular localization of proteins in various organisms. Natural Science, 2, 1090-1103. doi: 10.4236/ns.2010.210136.

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