KIS: An automated attribute induction method for classification of DNA sequences

Baten, A.K.M.A., Chang, B.C.H., Halgamuge, S.K. and Li, J. (2006). Splice site identification using probabilistic parameters and SVMclassification, BMC Bioinformatics 7(Suppl 5): S15, DOI:10.1186/1471-2105-7-S5-S15.10.1186/1471-2105-7-S5-S15176447117254299Search in Google Scholar

Berget, S.M., Moore, C. and Sharp, P.A. (1977). Spliced segments at the 5’ terminus of adenovirus 2 late mRNA, Proceedings of the National Academy of Sciences 74(8): 3171-3175.10.1073/pnas.74.8.3171431482269380Search in Google Scholar

Carrasco, R.C. and Oncina, J. (1994). Learning stochastic regular grammars by means of a state merging method, ICGI’94: Proceedings of the Second International Colloquium on Grammatical Inference and Applications, Alicante, Spain, pp. 139-152.Search in Google Scholar

Chen, T.-M., Lu, C.-C. and Li,W.-H. (2005). Prediction of splice sites with dependency graphs and their expanded Bayesian networks, Bioinformatics 21(4): 471-482.10.1093/bioinformatics/bti02515374869Search in Google Scholar

Davis, J. and Goadrich, M. (2006). The relationship between Precision-Recall and ROC curves, ICML’06: Proceedings of the 23rd International Conference on Machine Learning, Pittsburgh, PA, USA, pp. 233-240.Search in Google Scholar

Deshpande, M. and Karypis, G. (2002). Evaluation of techniques for classifying biological sequences, Pacific-Asia Conference on Knowledge Discovery and Data Mining, Taipei, Taiwan, pp. 417-431.Search in Google Scholar

Diederich, J. (2008). Rule Extraction from Support Vector Machines, Studies in Computational Intelligence, Vol. 80, Springer, Berlin/Heidelberg.Search in Google Scholar

Durbin, R., Eddy, S.R., Krogh, A. and Mitchison, G. (1998). Biological Sequence Analysis-Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, Cambridge.10.1017/CBO9780511790492Search in Google Scholar

Elsik, C.G., Worley, K.C., Zhang, L., Milshina, N.V., Jiang, H., Reese, J.T., Childs, K.L., Venkatraman, A., Dickens, C.M., Weinstock, G.M. and Gibbs, R.A. (2006). Community annotation: Procedures, protocols, and supporting tools, Genome Research 16(11): 1329-1333.10.1101/gr.558060617065605Search in Google Scholar

Kashiwabara, A.Y., Vieira, D.C.G., Machado-Lima, A. and Durham, A.M. (2007). Splice site prediction using stochastic regular grammars, GMR 6(1): 105-115.Search in Google Scholar

Michalewicz, Z. (1996). Genetic Algorithms + Data Structures = Evolution Programs, 3rd Edn., Springer-Verlag, London.Search in Google Scholar

Oncina, J. and Garcia, P. (1992). Inferring regular languages in polynomial update time, in A. Sanfeliu, N. P´erez de la Blanca and E. Vidal (Eds.), Pattern Recognition and Image Analysis, World Scientific Publishing, Singapore, pp. 49-61.Search in Google Scholar

Pesole, G., Grillo, G., Larizza, A. and Liuni, S. (2000). The untranslated regions of eukaryotic mRNAs: Structure, function, evolution and bioinformatic tools for their analysis, Briefings in Bioinformatics 1(3): 236-249.10.1093/bib/1.3.23611465035Search in Google Scholar

Quinlan, J.R. (1986). Induction of decision trees, Machine Learning 1(1): 81-106.10.1007/BF00116251Search in Google Scholar

Quinlan, J.R. (1993). C4.5: Programs for Machine Learning, Morgan Kaufmann Publishers, San Francisco, CA.Search in Google Scholar

R¨atsch, G. and Sonnenburg, S. (2004). Accurate Splice Site Detection for Caenorhabditis Elegans, MIT Press, Cambridge, MA.Search in Google Scholar

R¨atsch, G., Sonnenburg, S. and Sch¨olkopf, B. (2005). RASE: Recognition of alternatively spliced exons in C. elegans, Bioinformatics 21(Suppl 1): i369-i377.Search in Google Scholar

Reese, M.G., Eeckman, F.H., Kulp, D. and Haussler, D. (1997). Improved splice site detection in Genie, Journal of Computational Biology 4(3): 311-324.10.1089/cmb.1997.4.3119278062Search in Google Scholar

Ron, D., Singer, Y. and Tishby, N. (1996). The power of amnesia: Learning probabilistic automata with variable memory length, Machine Learning 25(2): 117-149.10.1007/BF00114008Search in Google Scholar

Ron, D., Singer, Y. and Tishby, N. (1998). On the learnability and usage of acyclic probabilistic finite automata, Journal of Computer and System Sciences 56(2): 133-152.10.1006/jcss.1997.1555Search in Google Scholar

Sonnenburg, S. (2009). Machine Learning for Genomic Sequence Analysis, Ph.D. thesis, Technischen Universit¨at Berlin, Berlin.Search in Google Scholar

Sonnenburg, S., Schweikert, G., Philips, P., Behr, J. and R¨atsch, G. (2007). Accurate splice site prediction using support vector machines, BMC Bioinformatics 8(Suppl 10): S7.10.1186/1471-2105-8-S10-S7223050818269701Search in Google Scholar

Tickle, A., Andrews, R., Golea, M. and Diederich, J. (1998). The truth will come to light: Directions and challenges in extracting the knowledge embedded within trained artificial neural networks, IEEE Transactions on Neural Networks 9(6): 1057-1068.10.1109/72.72835218255792Search in Google Scholar