### Abstract

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 such that they satisfy the size bounds and the total weight of the tiles is maximized. This solution to this problem is important to a number of computational biology applications, such as selecting genomic DNA fragments for amplicon microarrays, or 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 discuss the solution of 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 our tiling problems. We also discuss NPhardness and approximation algorithms for generalization of our basic tiling problem to higher dimensions.

Original language | English (US) |
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Title of host publication | Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings |

Editors | Roderic Guigo, Dan Gusfield |

Publisher | Springer Verlag |

Pages | 419-433 |

Number of pages | 15 |

ISBN (Print) | 3540442111, 9783540442110 |

State | Published - Jan 1 2002 |

Event | 2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 - Rome, Italy Duration: Sep 17 2002 → Sep 21 2002 |

### Publication series

Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
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Volume | 2452 |

ISSN (Print) | 0302-9743 |

ISSN (Electronic) | 1611-3349 |

### Other

Other | 2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 |
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Country | Italy |

City | Rome |

Period | 9/17/02 → 9/21/02 |

### Fingerprint

### All Science Journal Classification (ASJC) codes

- Theoretical Computer Science
- Computer Science(all)

### Cite this

*Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings*(pp. 419-433). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2452). Springer Verlag.

}

*Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings.*Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2452, Springer Verlag, pp. 419-433, 2nd International Workshop on Algorithms in Bioinformatics, WABI 2002, Rome, Italy, 9/17/02.

**Fast optimal genome tiling with applications to microarray design and homology search.** / Berman, Piotr; Bertone, Paul; DasGupta, Bhaskar; Gerstein, Mark; Kao, Ming Yang; Snyder, Michael.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - Fast optimal genome tiling with applications to microarray design and homology search

AU - Berman, Piotr

AU - Bertone, Paul

AU - DasGupta, Bhaskar

AU - Gerstein, Mark

AU - Kao, Ming Yang

AU - Snyder, Michael

PY - 2002/1/1

Y1 - 2002/1/1

N2 - 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 such that they satisfy the size bounds and the total weight of the tiles is maximized. This solution to this problem is important to a number of computational biology applications, such as selecting genomic DNA fragments for amplicon microarrays, or 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 discuss the solution of 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 our tiling problems. We also discuss NPhardness and approximation algorithms for generalization of our basic tiling problem to higher dimensions.

AB - 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 such that they satisfy the size bounds and the total weight of the tiles is maximized. This solution to this problem is important to a number of computational biology applications, such as selecting genomic DNA fragments for amplicon microarrays, or 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 discuss the solution of 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 our tiling problems. We also discuss NPhardness and approximation algorithms for generalization of our basic tiling problem to higher dimensions.

UR - http://www.scopus.com/inward/record.url?scp=84957007909&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84957007909&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:84957007909

SN - 3540442111

SN - 9783540442110

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 419

EP - 433

BT - Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings

A2 - Guigo, Roderic

A2 - Gusfield, Dan

PB - Springer Verlag

ER -