Identifying CpG Islands in Genome Using Conditional Random Fields
This paper presents a novel method for CpG islands location identification based on conditional random fields (CRF) model. The method transforms CpG islands location identification into the problem of sequential data labeling. Based on the nature of CpG islands location, we design the methods of model constructing, training and decoding in CRF accordingly. Experimental results on benchmark data sets show that our algorithm is more practicable and efficient than the traditional methods.
Keywordsconditional random fields model CpG islands sequential data labeling
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- 1.Li, W.J., Li, M., Xin, R.H., Wei, L.H.: Promoter Recognition in Human Genome Based on KL Divergence and BP Neural Network. Journal of Liaoning Normal University (Natural Science Edition) 3(33), 42–45 (2010)Google Scholar
- 2.Huang, Y.K.: Promoter Recognition System Research from Gene Sequence Data. The Master’s Thesis of Harbin Engineering University (2009)Google Scholar
- 3.Zhang, C.T.: The Current Status and The Prospect of Bioinformatics. The Journal of Liaoning Science and Technology 08, 25–26 (2001)Google Scholar
- 4.Tong, Q., Zhen, H.R., Ning, Y.: A Gene-prediction Algorithm Based on the Statistical Combination and the Classification in Terms of CpG Content. Journal of Beijing Biomedical Engineering 4(26), 178–181 (2007)Google Scholar
- 8.Wang, J.L., Su, J.Z., Wang, F.C., Ying, Z.Y.: A New Method to Predict CpG-islands Based on Fuzzy Theory. China Journal of Bioinformatics 6(7), 91–94 (2009)Google Scholar
- 9.Shi, O.Y., Yang, J., Tian, X.: Hidden Markov Model for CpG Islands Prediction Based on Matlab. Computer Applications and Software 11(25), 214–215 (2008)Google Scholar
- 10.Jiang, H.J., Zhang, Z.L.: Discrimination of CpG Islands Location Based on HMM. Mathematical Theory and Applications 6(29), 113–116 (2009)Google Scholar
- 11.John, L., Andrew, M.C., Fernando, P.: Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data. In: Proc. of the 18th ICML, pp. 282–289. Morgan Kaufmann, San Francisco (2001)Google Scholar
- 12.Hammersley, J.M., Clifford, P.: Markov Field on Finite Graphs and Lattices (1971) (unpublished)Google Scholar