Hello. Sign in to personalize your visit. New user? Register now.  
GEN Updates in Biotechnology - Next-Generation Sequencing
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.

Full Text PDF: • HiRes for printing (154.5 KB) • PDF Plus w/ links (187.7 KB)


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.

Free first page

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 & Permissions
Current awareness on comparative and functional genomics
Comparative and Functional Genomics. 2005, Vol. 6, No. 1-2: 97
CrossRef
All papers
Previous Next