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Identifying the singleplex and multiplex proteins based on transductive learning for protein subcellular localization prediction

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Abstract

A new method is proposed to identify whether a query protein is singleplex or multiplex for improving the quality of protein subcellular localization prediction. Based on the transductive learning technique, this approach utilizes the information from the both query proteins and known proteins to estimate the subcellular location number of every query protein so that the singleplex and multiplex proteins can be recognized and distinguished. Each query protein is then dealt with by a targeted single-label or multi-label predictor to achieve a high-accuracy prediction result. We assess the performance of the proposed approach by applying it to three groups of protein sequences datasets. Simulation experiments show that the proposed approach can effectively identify the singleplex and multiplex proteins. Through a comparison, the reliably of this method for enhancing the power of predicting protein subcellular localization can also be verified.

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Acknowledgments

This work is supported by the National Natural Science Foundation of China (61174027); National Science and Technology Mega-Project Program of China (2010ZX04007-011-5); Program for Liaoning Excellent Talents in University (LJQ2012005); Specialized Research Fund for the Doctoral Program of Higher Education (20120041110008).

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Correspondence to Wenqi Liu.

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Cao, J., Liu, W., He, J. et al. Identifying the singleplex and multiplex proteins based on transductive learning for protein subcellular localization prediction. Biotechnol Lett 35, 1107–1113 (2013). https://doi.org/10.1007/s10529-013-1186-6

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  • DOI: https://doi.org/10.1007/s10529-013-1186-6

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