Splice sites detection by combining Markov and hidden Markov model

Proceedings of the 2009 2nd International Conference on Biomedical Engineering and Informatics, BMEI 2009

Volumn , Issue , 2009, Pages

  Zhang, Quanwei ^a   Peng, Qinke ^a   Li, Kankan ^a   Kang, Xuejiao ^a   Li, Jing ^a  

^a XI'AN JIAOTONG UNIVERSITY   (China)

Author keywords

Hidden markov model; Markov model; Splice sites detection; Support vector machine

Indexed keywords

BIOLOGICAL DATA; BIOLOGICAL FEATURES; CONVENTIONAL MODELS; DETECTING METHODS; DINUCLEOTIDES; ENSEMBLE MODELS; GENE PRODUCTS; GENE STRUCTURE; MARKOV MODEL; SPLICE SITE; SPLICE SITES DETECTION; TIME COST;

BIOINFORMATICS; IMAGE RETRIEVAL; SUPPORT VECTOR MACHINES;

HIDDEN MARKOV MODELS;

EID: 74049096795     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BMEI.2009.5301970     Document Type: Conference Paper

References (21)

1. Burset M., Seledtsov I.A., and Solovyev V.V., 'Analysis of canonical and non-canonical splice sites in mammalian genomes', Nucleic Acids Res, 2000, 28, (21), pp. 4364-4375.
2. Rajapakse J.C., and Ho L.S., 'Markov encoding for detecting signals in genomic sequences', Ieee-Acm Transactions on Computational Biology and Bioinformatics, 2005, 2, (2), pp. 131-142.
3. Chen T.M., Lu C.C., and Li W.H., 'Prediction of splice sites with dependency graphs and their expanded bayesian networks', Bioinformatics, 2005, 21, (4), pp. 471-482.
4. Zhang L.R., and Luo L.F., 'Splice site prediction with quadratic discriminant analysis using diversity measure', Nucleic Acids Res, 2003, 31, (21), pp. 6214-6220.
5. Baten A.K.M.A., Chang B.C.H., Halgamuge S.K., and Li J., 'Splice site identification using probabilistic parameters and SVM classification', Bmc Bioinformatics, 2006, 7, pp. S15.
6. Zhang Y., Chu C.H., Chen Y.X., Zha H.Y., and Ji X., 'Splice site prediction using support vector machines with a Bayes kernel', Expert Syst Appl, 2006, 30, (1), pp. 73-81.
7. Xia H.Y., Zhou Q., and Li Y.D., 'Application of hidden Markov model in the recognition of splicing sites', Journal of Tsinghua University(Science and Technology), 2002, 42, (9), pp. 1214-1217.
8. Yin M.M., and Wang J.T.L., 'Effective hidden Markov models for detecting splicing junction sites in DNA sequences', Information sciences, 2001, 139, pp. 139-163.
9. Feng X.C., Qian M.P., Deng M.H., Ma X.T., and Yan X.T., 'Application of Hidden Semi-Markov Model to 3́ Splice Sites Identification', Progress In Biochemistry and Biophysics, 2004, 31, (5), pp. 455-458.
10. Baten A.K.M.A., Halgamuge S.K., and Chang B.C.H., 'Fast splice site detection using information content and feature reduction', Bmc Bioinformatics, 2008, 9, (Supp l2), pp.: S8.
11. Buratti E., and Baralle F.E., 'Influence of RNA secondary structure on the pre-mRNA splicing process', Molecular and Cellular Biology, 2004, 24, (24), pp. 10505-10514.
12. Marashi S.A., Eslahchi C., Pezeshk H., and Sadeghi M., 'Impact of RNA structure on the prediction of donor and acceptor splice sites', Bmc Bioinformatics, 2006, 7, pp. 297.
13. Hongmei Z., Jiaxin W., Yannan Z., and Zehong Y., 'Application of Time-delay HMM in Gene Splice Donor Sites Prediction', Computer Engineering, 2007, 33, (5), pp. 1-3.
14. Zhang X.H.F., Heller K.A., Hefter L., Leslie C.S., and Chasin L.A., 'Sequence information for the splicing of human Pre-mRNA identified by support vector machine classification', Genome Res, 2003, 13, (12), pp. 2637-2650.
15. Zhang Q.W., Peng Q.K., and Xu T., 'DNA splice site sequences clustering method for conservativeness analysis', Prog. Nat. Sci., 2009, 19, (4), pp. 511-516.
16. Shen H.B., and Chou K.C., 'Hum-mPLoc: An ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites', Biochemical and Biophysical Research Communications, 2007, 355, (4), pp. 1006-1011.
17. Dietterich T.G., 'An experimental comparison of three methods for constructing ensembles of decision trees: Bagging, boosting, and randomization', Machine Learning, 2000, 40, (2), pp. 139-157.
18. Ranawana R., and Palade V., 'Multi-Classifier Systems - A Review and Roadmap for Developers', Journal of Hybrid Intelligent Systems, 2006, 3, (1), pp. 27.
19. Zhang C.T., and Zhang R., 'Evaluation of gene-finding algorithms by a content-balancing accuracy index', J Biomol Struct Dyn, 2002, 19, (6), pp. 1045-1052.
20. Saeys Y., Degroeve S., Aeyels D., Van De Peer Y., and Rouze P., 'Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction', Bioinformatics, 2003, 19, pp. ii179-188.
21. Chang C.-C., and Lin C.-J., 'LIBSVM : a library for support vector machines.Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm', 2001.