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Int. J. Mol. Sci. 2012, 13(3), 3650-3660; doi:10.3390/ijms13033650

Prediction of Bioluminescent Proteins Using Auto Covariance Transformation of Evolutional Profiles

1
School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
2
School of Life Sciences, Northeast Normal University, Changchun 130024, China
3
National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun 130024, China
*
Authors to whom correspondence should be addressed.
Received: 10 January 2012 / Revised: 21 February 2012 / Accepted: 5 March 2012 / Published: 19 March 2012
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Abstract

Bioluminescent proteins are important for various cellular processes, such as gene expression analysis, drug discovery, bioluminescent imaging, toxicity determination, and DNA sequencing studies. Hence, the correct identification of bioluminescent proteins is of great importance both for helping genome annotation and providing a supplementary role to experimental research to obtain insight into bioluminescent proteins’ functions. However, few computational methods are available for identifying bioluminescent proteins. Therefore, in this paper we develop a new method to predict bioluminescent proteins using a model based on position specific scoring matrix and auto covariance. Tested by 10-fold cross-validation and independent test, the accuracy of the proposed model reaches 85.17% for the training dataset and 90.71% for the testing dataset respectively. These results indicate that our predictor is a useful tool to predict bioluminescent proteins. This is the first study in which evolutionary information and local sequence environment information have been successfully integrated for predicting bioluminescent proteins. A web server (BLPre) that implements the proposed predictor is freely available.
Keywords: bioluminescent proteins; position specific scoring matrix; support vector machine; evolutionary information bioluminescent proteins; position specific scoring matrix; support vector machine; evolutionary information
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Zhao, X.; Li, J.; Huang, Y.; Ma, Z.; Yin, M. Prediction of Bioluminescent Proteins Using Auto Covariance Transformation of Evolutional Profiles. Int. J. Mol. Sci. 2012, 13, 3650-3660.

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