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Plant Methods. 2012 Feb 3;8:5. doi: 10.1186/1746-4811-8-5.

PhosphoRice: a meta-predictor of rice-specific phosphorylation sites.

Que S#1,2, Li K#2, Chen M#2, Wang Y2, Yang Q2, Zhang W1,2, Zhang B1,2, Xiong B3, He H1,2.

Author information

1
Key Laboratory of Ministry of Education for Genetic, Breeding and Multiple Utilization of Crops, Fuzhou 350002, China.
2
College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
3
Key Laboratory of Nondestructive Test of Ministry of Education, Nanchang Hangkong University, Nanchang 330063, China.
#
Contributed equally

Abstract

BACKGROUND:

As a result of the growing body of protein phosphorylation sites data, the number of phosphoprotein databases is constantly increasing, and dozens of tools are available for predicting protein phosphorylation sites to achieve fast automatic results. However, none of the existing tools has been developed to predict protein phosphorylation sites in rice.

RESULTS:

In this paper, the phosphorylation site predictors, NetPhos 2.0, NetPhosK, Kinasephos, Scansite, Disphos and Predphosphos, were integrated to construct meta-predictors of rice-specific phosphorylation sites using several methods, including unweighted voting, unreduced weighted voting, reduced unweighted voting and weighted voting strategies. PhosphoRice, the meta-predictor produced by using weighted voting strategy with parameters selected by restricted grid search and conditional random search, performed the best at predicting phosphorylation sites in rice. Its Matthew's Correlation Coefficient (MCC) and Accuracy (ACC) reached to 0.474 and 73.8%, respectively. Compared to the best individual element predictor (Disphos_default), PhosphoRice archieved a significant increase in MCC of 0.071 (P < 0.01), and an increase in ACC of 4.6%.

CONCLUSIONS:

PhosphoRice is a powerful tool for predicting unidentified phosphorylation sites in rice. Compared to the existing methods, we found that our tool showed greater robustness in ACC and MCC. PhosphoRice is available to the public at http://bioinformatics.fafu.edu.cn/PhosphoRice.

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