### Abstract

Let S and T be two finite sets of points on the real line with |S|+|T|=n and |S|>|T|. The restriction scaffold assignment problem in computational biology assigns each point of S to a point of T such that the sum of all the assignment costs is minimized, with the constraint that every element of T must be assigned at least one element of S. The cost of assigning an element si of S to an element tj of T is |s_{i} - t_{j}|, i.e., the distance between si and tj. In 2003 Ben-Dor, Karp, Schwikowski and Shamir [J. Comput. Biol. 10 (2) (2003) 385] published an O(nlogn) time algorithm for this problem. Here we provide a counterexample to their algorithm and present a new algorithm that runs in O(n2) time, improving the best previous complexity of O(n3).

Original language | English (US) |
---|---|

Pages (from-to) | 466-471 |

Number of pages | 6 |

Journal | Information Processing Letters |

Volume | 95 |

Issue number | 4 |

DOIs | |

State | Published - Aug 31 2005 |

### Fingerprint

### Keywords

- Analysis of algorithms
- Assignment problems
- Computational biology
- Computational geometry
- Information retrieval
- Operations research
- Rhythmic similarity measures

### ASJC Scopus subject areas

- Computational Theory and Mathematics

### Cite this

**An algorithm for computing the restriction scaffold assignment problem in computational biology.** / Colannino, Justin; Toussaint, Godfried.

Research output: Contribution to journal › Article

*Information Processing Letters*, vol. 95, no. 4, pp. 466-471. https://doi.org/10.1016/j.ipl.2005.05.007

}

TY - JOUR

T1 - An algorithm for computing the restriction scaffold assignment problem in computational biology

AU - Colannino, Justin

AU - Toussaint, Godfried

PY - 2005/8/31

Y1 - 2005/8/31

N2 - Let S and T be two finite sets of points on the real line with |S|+|T|=n and |S|>|T|. The restriction scaffold assignment problem in computational biology assigns each point of S to a point of T such that the sum of all the assignment costs is minimized, with the constraint that every element of T must be assigned at least one element of S. The cost of assigning an element si of S to an element tj of T is |si - tj|, i.e., the distance between si and tj. In 2003 Ben-Dor, Karp, Schwikowski and Shamir [J. Comput. Biol. 10 (2) (2003) 385] published an O(nlogn) time algorithm for this problem. Here we provide a counterexample to their algorithm and present a new algorithm that runs in O(n2) time, improving the best previous complexity of O(n3).

AB - Let S and T be two finite sets of points on the real line with |S|+|T|=n and |S|>|T|. The restriction scaffold assignment problem in computational biology assigns each point of S to a point of T such that the sum of all the assignment costs is minimized, with the constraint that every element of T must be assigned at least one element of S. The cost of assigning an element si of S to an element tj of T is |si - tj|, i.e., the distance between si and tj. In 2003 Ben-Dor, Karp, Schwikowski and Shamir [J. Comput. Biol. 10 (2) (2003) 385] published an O(nlogn) time algorithm for this problem. Here we provide a counterexample to their algorithm and present a new algorithm that runs in O(n2) time, improving the best previous complexity of O(n3).

KW - Analysis of algorithms

KW - Assignment problems

KW - Computational biology

KW - Computational geometry

KW - Information retrieval

KW - Operations research

KW - Rhythmic similarity measures

UR - http://www.scopus.com/inward/record.url?scp=21344443505&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=21344443505&partnerID=8YFLogxK

U2 - 10.1016/j.ipl.2005.05.007

DO - 10.1016/j.ipl.2005.05.007

M3 - Article

AN - SCOPUS:21344443505

VL - 95

SP - 466

EP - 471

JO - Information Processing Letters

JF - Information Processing Letters

SN - 0020-0190

IS - 4

ER -