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April 1994 (Vol. 9, No. 2)   pp. 2-10
Machine Learning Approaches to Gene Recognition

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DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/64.294127
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Abstract
As laboratories round the world produce ever-greater volumes of DNA sequence data, efficient computational analysis techniques are becoming essential. This article surveys several efforts that apply machine learning techniques to gene recognition. Machine learning methods are well suited to sequence analysis because they can learn useful descriptions of genetic concepts when given only instances, rather than explicit definitions, of those concepts. This article looks at several such approaches to gene recognition in two broad classes: search by signal and search by content.
References
[1] G.D. Stormo et al., "Use of the Perceptron Algorithm to Distinguish Translational Initiation Sites inE. coli," Nucleic Acids Research, Vol. 10, No. 9, 1982, pp. 2997-3011.
[2] G. Towell, J. Shavlik, and M. Noordewier, "Refinement of Approximate Domain Theories by Knowledge-Based Neural Networks,"Proc. Eighth Nat'l Conf. Artificial Intelligence, AAAI Press, Menlo Park, Calif., 1990, pp. 861-866.
[3] A. Lapedes et al., "Application of Neural Networks and Other Machine Learn ing Algorithms to DNA Sequence Analysis," inComputers and DNA, SFI Studies in the Sciences of Complexity, Vol. VII, G. Bell and T. Marr, eds., Addison-Wesley, Reading, Mass., 1989, pp. 157-182.
[4] J. R. Quinlan, "Induction of decision trees,"Machine Learning, vol. 1, no. 1, pp. 81-106, 1986.
[5] T. Cover and P. Hart, "Nearest neighbor pattern classification,"IEEE Trans. Inform. Theory, vol. IT-13, pp. 21-27, 1967.
[6] R. Staden and A.D. McLachlan, "Codon Preference and Its Use in Identifying Protein Coding Regions in Long DNA Sequences,"Nucleic Acids Research, Vol. 10, No. 1, 1982, pp. 141-156.
[7] M. Borodovsky and J. McIninch, "Prediction of Gene Locations Using DNA Markov Chain Models,"Proc. Second Int'l Conf. Bioinformatics, Supercomputing, and Complex Genome Analysis, World Scientific, Singapore, 1993, pp. 231-248.
[8] R. Farber, A. Lapedes, and K. Sirotkin, "Determination of Eucaryotic Protein Coding Regions Using Neural Networks and Information Theory,"J. Molecular Biology, Vol. 226, No. 2, 1992, pp. 471-479.
[9] E.C. Uberbacher and R.J. Mural, "Locating Protein Coding Regions in Human DNA Sequences by a Multiple-Sensor-Neural Network Approach,"Proc. Nat'l Academy of Sciences, Vol. 88, No. 24, 1991, pp. 11261-11265.
[10] E.C. Uberbacher et al., "Gene Recognition and Assembly in the Grail System: Progress and Challenges,"Proc. Second Int'l Conf. Bioinformatics, Supercomputing, and Complex Genome Analysis, World Scientific, Singapore, 1993, pp. 465-476.
[11] S.F. Altschul et al., "Basic Local Alignment Search Tool,"J. Molecular Biology, Vol. 215, No. 3, 1990, pp. 403-410.
[12] L. Hunter, N. Harris, and D.J. States, "Efficient Classification of Massive, Unsegmented Datastreams,"Proc. Ninth Int'l Conf. Machine Learning, Morgan Kaufmann, San Mateo, Calif., 1992, pp. 224-232.
[13] N.L. Harris, D.J. States, and L. Hunter, "ClassX: A Browsing Tool for Protein Sequence Megaclassification,"Proc. 26th Hawaii Int'l Conf. System Sciences, IEEE Computer Society Press, Los Alamitos, Calif., 1993, pp. 554-563.
[14] R. Guigo et al., "Prediction of Gene Structure,"J. Molecular Biology, Vol. 226, No. 1, 1992, pp. 141-157.
[15] E.E. Snyder and G.D. Stormo, "Identification of Coding Regions in Genomic DNA Sequences: An Application of Dynamic Programming and Neural Networks,"Nucleic Acids Research, Vol. 21, No. 3, 1993, pp. 607-613.
[16] L. Hunter, D. Searls, and J. Shavlik, eds.,Proc. First Int'l Conf. Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, Calif., 1993.
Additional Information

Citation:  Mark W. Craven, Jude W. Shavlik, "Machine Learning Approaches to Gene Recognition," IEEE Expert: Intelligent Systems and Their Applications, vol. 09,  no. 2,  pp. 2-10,  Apr.,  1994

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