Gene Ontology-Based Protein Function Prediction by Using Sequence Composition Information

Author(s): Qiwen Dong, Shuigeng Zhou, Lei Deng, Jihong Guan.

Journal Name: Protein & Peptide Letters

Volume 17 , Issue 6 , 2010

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The prediction of protein function is a difficult and important problem in computational biology. In this study, an efficient method is presented to predict protein function with sequence composition information. Four kinds of basic building blocks of protein sequences are investigated, including N-grams, binary profiles, PFAM domains and InterPro domains. The protein sequences are mapped into high-dimensional vectors by using the occurrence frequencies of each kind of building blocks. The resulting vectors are then taken as input to support vector machine to predict their function based on gene ontology. Experiments are conducted over the subset of GOA database. The experimental results show that the protein function can be predicted from primary sequence information. The method based on InterPro domains outperforms the other building blocks, and gets an overall accuracy of 0.87 and ROC score is 0.93. We also demonstrate that the use of feature extraction algorithms such as latent semantic analysis and nonnegative matrix factorization, can efficiently remove noise and improve the prediction efficiency without significantly degrading the performance. The results obtained here are helpful for the prediction of protein function by using only sequence information.

Keywords: Protein function prediction, basic building block, support vector machine

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Article Details

Year: 2010
Page: [789 - 795]
Pages: 7
DOI: 10.2174/092986610791190336
Price: $65

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