An Optimal DNA Segmentation Based on the MDL Principle

Stanford, California August 11-August 14

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http://doi.ieeecomputersociety.org/10.1109/CSB.2003.1227402

IEEE Computer Society Bioinformatics ...

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	Wojciech Szpankowski, Wenhui Ren, Lukasz Szpankowski, "An Optimal DNA Segmentation Based on the MDL Principle," Computational Systems Bioinformatics Conference, International IEEE Computer Society, pp. 541, IEEE Computer Society Bioinformatics Conference (CSB'03), 2003.

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	@article{ 10.1109/CSB.2003.1227402, author = {Wojciech Szpankowski and Wenhui Ren and Lukasz Szpankowski}, title = {An Optimal DNA Segmentation Based on the MDL Principle}, journal ={Computational Systems Bioinformatics Conference, International IEEE Computer Society}, volume = {0}, year = {2003}, isbn = {0-7695-2000-6}, pages = {541}, doi = {http://doi.ieeecomputersociety.org/10.1109/CSB.2003.1227402}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }

	RefWorks Procite/RefMan/Endnote	x
	TY - CONF JO - Computational Systems Bioinformatics Conference, International IEEE Computer Society TI - An Optimal DNA Segmentation Based on the MDL Principle SN - 0-7695-2000-6 SP EP A1 - Wojciech Szpankowski, A1 - Wenhui Ren, A1 - Lukasz Szpankowski, PY - 2003 KW - null VL - 0 JA - Computational Systems Bioinformatics Conference, International IEEE Computer Society ER -

Wojciech Szpankowski, Purdue University

Wenhui Ren, Purdue University

Lukasz Szpankowski, University of Michigan

The biological world is highly stochastic as well as inhomogeneous in its behavior. The transition between homogeneous and inhomogeneous regions of DNA, known also as change points, carry important biological information. Our goal is to employ rigorous methods of information theory to quantify structural properties of DNA sequences. In particular, we adopt the Stein-Ziv lemma to find asymptotically optimal discriminant function that determines whether two DNA segments are generated by the same source and assuring exponentially small false positives. Then we apply the Minimum Description Length (MDL) principle to select parameters of our segmentation algorithm. Finally, we perform extensive experimental work on human chromosome 9. After grouping A and G (purines) and T and C (pyrimidines) we discover change points between coding and noncoding regions as well as the beginning of a CpG island.

Citation:

Wojciech Szpankowski, Wenhui Ren, Lukasz Szpankowski, "An Optimal DNA Segmentation Based on the MDL Principle," csb, pp.541, IEEE Computer Society Bioinformatics Conference (CSB'03), 2003

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