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iLoc-Gpos: A Multi-Layer Classifier for Predicting the Subcellular Localization of Singleplex and Multiplex Gram-Positive Bacterial Proteins

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By introducing the “multi-layer scale”, as well as hybridizing the information of gene ontology and the sequential evolution information, a novel predictor, called iLoc-Gpos, has been developed for predicting the subcellular localization of Gram positive bacterial proteins with both single-location and multiple-location sites. For facilitating comparison, the same stringent benchmark dataset used to estimate the accuracy of Gpos-mPLoc was adopted to demonstrate the power of iLoc-Gpos. The dataset contains 519 Gram-positive bacterial proteins classified into the following four subcellular locations: (1) cell membrane, (2) cell wall, (3) cytoplasm, and (4) extracell; none of proteins included has ≥25% pairwise sequence identity to any other in a same subset (subcellular location). The overall success rate by jackknife test on such a stringent benchmark dataset by iLoc-Gpos was over 93%, which is about 11% higher than that by GposmPLoc. As a user-friendly web-server, iLoc-Gpos is freely accessible to the public at Gpos or Meanwhile, a step-by-step guide is provided on how to use the web-server to get the desired results. Furthermore, for the user’s convenience, the iLoc-Gpos web-server also has the function to accept the batch job submission, which is not available in the existing version of Gpos-mPLoc web-server.

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Keywords: Absolute true success rate; FASTA format; Gene ontology; Gpos-PLoc; K-Nearest Neighbor; KNN classifier; Mahalanobis; Multi-layer scale; Multiplex proteins; PSI-BLAST; PSSM; PseAAC; Singleplex proteins; jackknife test; post-genomic era

Document Type: Research Article

Publication date: January 1, 2012

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.
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