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Journal of Computational Biology
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search
To cite this paper:
Piotr Berman, Paul Bertone, Bhaskar Dasgupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder.
Journal of Computational Biology.
August 1, 2004,
11(4): 766-785.
doi:10.1089/cmb.2004.11.766.
Piotr Berman Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802. Paul Bertone Department of Molecular, Cellular, and Developmental Biology and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520. Bhaskar Dasgupta Department of Computer Science, University of Illinois at Chicago, Chicago, IL 60607. Mark Gerstein Department of Molecular Biophysics and Biochemistry and Department of Computer Science, Yale University, New Haven, CT 06520. Ming-Yang Kao Department of Computer Science, Northwestern University, Evanston, IL 60201. Michael Snyder Department of Molecular, Cellular, and Developmental Biology and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520. In this paper, we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size-bound parameters, we want to find a set of tiles of maximum total weight such that each tiles satisfies the size bounds. A solution to this problem is important to a number of computational biology applications such as selecting genomic DNA fragments for PCR-based amplicon microarrays and performing homology searches with long sequence queries. Our goal is to design efficient algorithms with linear or near-linear time and space in the normal range of parameter values for these problems. For this purpose, we first discuss the solution to a basic online interval maximum problem via a sliding-window approach and show how to use this solution in a nontrivial manner for many of the tiling problems introduced.We also discuss NP-hardness results and approximation algorithms for generalizing our basic tiling problem to higher dimensions. Finally, computational results from applying our tiling algorithms to genomic sequences of five model eukaryotes are reported.  This paper was cited by:GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data Brendan J. Frey, Quaid D. Morris, Timothy R. Hughes Journal of Computational Biology. Mar 2006, Vol. 13, No. 2: 200-214 Abstract | Full Text PDF | Reprints & PermissionsCurrent awareness on comparative and functional genomics Comparative and Functional Genomics. 2005, Vol. 6, No. 1-2: 97 CrossRef
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