## Physical Mapping of Chromosomes Using Unique Probes (1994)

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Venue: | Proceedings of the 5th ACM-SIAM Symposium on Discrete Algorithms (SODA ’94 |

Citations: | 47 - 0 self |

### BibTeX

@INPROCEEDINGS{Alizadeh94physicalmapping,

author = {Farid Alizadeh and Richard M. Karp and Deborah K. Weisser and Geoffrey Zweig},

title = {Physical Mapping of Chromosomes Using Unique Probes},

booktitle = {Proceedings of the 5th ACM-SIAM Symposium on Discrete Algorithms (SODA ’94},

year = {1994},

pages = {489--500},

publisher = {ACM Press}

}

### Years of Citing Articles

### OpenURL

### Abstract

this paper we present several combinatorial algorithms for reconstructing a DNA strand given a collection of overlapping fragments of the strand. A human chromosome, which is a DNA molecule of about 10

### Citations

467 |
Testing for the consecutive ones property, interval graphs, and graph planarity using PQ-tree algorithms
- Booth, Leuker
- 1976
(Show Context)
Citation Context ...s to determine probe ordering, given data for each clone indicating which probes occur on it. In the absence of errors, the correct orderings can be found very easily using the PQ-tree data structure =-=[BL76]-=- to generate the set of all arrangements of probes consistent with the data. The data is never free from error however, and algorithms are differentiated by their performance in the presence of errors... |

377 |
Simulated Annealing: Theory and Applications
- Laarhoven, Aarts
- 1987
(Show Context)
Citation Context ... moves equal to twice the fraction of random moves that cause improvement. Other than in setting the initial temperature, we use a conventional cooling schedule and a conventional stopping rule [L88] =-=[AL87]-=-. The maximum number of moves considered at each temperature step is 20 times the number of STSs. The temperature is multiplied by 0.95 as soon as this number of moves have been attempted, or when 25%... |

52 | Physical mapping of chromosomes: A combinatorial problem in molecular biology. Algorithmica
- Alizadeh, Karp, et al.
- 1995
(Show Context)
Citation Context ...tion of the rows which minimizes the number of gaps will correspond to a good probe ordering. Minimizing the number of gaps can be cast as a Traveling-Salesman Problem called the Hamming Distance TSP =-=[AKNW91]-=-, in which the cities are the rows of A together with an additional row of n zeroes, and the distance between two cities is the Hamming distance between the corresponding rows; i.e., the number of pos... |

29 |
Statistical methods for multipoint radiation hybrid mapping
- Boehnke, Lange, et al.
- 1991
(Show Context)
Citation Context ...h procedure based on random clone reversals is described, and found to outperform a simulated annealing implementation. The Hamming distance metric has seen extensive use in radiation hybrid mapping; =-=[MBC91]-=- provides a comparison with other methods in that context. [GI94] presents two algorithms for ordering probes when the data is contaminated with chimeric fragments, but not false positives or false ne... |

25 |
Theoretical and computational aspects of simulated annealing
- Laarhoven
- 1988
(Show Context)
Citation Context ...of the moves equal to twice the fraction of random moves that cause improvement. Other than in setting the initial temperature, we use a conventional cooling schedule and a conventional stopping rule =-=[L88]-=- [AL87]. The maximum number of moves considered at each temperature step is 20 times the number of STSs. The temperature is multiplied by 0.95 as soon as this number of moves have been attempted, or w... |

19 | The human Y chromosome: Overlapping DNA clones spanning the euchromatic region, Science 258 - Foote, Vollrath, et al. - 1992 |

17 |
PQ Tree Algorithms
- Booth
- 1975
(Show Context)
Citation Context ...Lc(A) + Md(A). Section 3.1 describes an effective algorithm to find a good solution of this optimization problem. The problem is NP-complete even in the absence of false positives and chimeric clones =-=[B75]. 2 -=-Algorithmic Approaches We present several approaches to the problem of recovering the underlying data A and the permutations�� from the measured data D. 2.1 The Maximum Posterior Probability Metho... |

13 |
A fast random cost algorithm for physical mapping
- Wang, A, et al.
- 1994
(Show Context)
Citation Context ...s a simulated annealing approach to ordering clones by minimizing the Hamming distance summed over consecutive pairs of clones. The Hamming distance objective function is also used to order clones in =-=[YWA94]-=-. A heuristic search procedure based on random clone reversals is described, and found to outperform a simulated annealing implementation. The Hamming distance metric has seen extensive use in radiati... |

8 | The chimeric mapping problem: Algorithmic strategies and performance evaluation on synthetic genomic data
- Greenberg, Istrail
- 1995
(Show Context)
Citation Context ...d to outperform a simulated annealing implementation. The Hamming distance metric has seen extensive use in radiation hybrid mapping; [MBC91] provides a comparison with other methods in that context. =-=[GI94] pre-=-sents two algorithms for ordering probes when the data is contaminated with chimeric fragments, but not false positives or false negatives. The first of these approaches is based on minimizing ��,... |

6 |
ODS: Ordering DNA sequences ± A physical mapping algorithm based on simulated annealing, CABIOS 9
- Cuticchia, Arnold, et al.
- 1993
(Show Context)
Citation Context ...tive fashion. Our computational results are summarized in Section 7. vii 2.6 Relationship to Previous Work In the field of physical mapping, simulated annealing has been used by [RML93], [AGL94], and =-=[ACT93]-=-, among others. [RML93] presents a software package used to construct a YAC map of S. pombe. This package uses simulated annealing to minimize a distance measure, d ab = nab \Gammar ab nab , summed ov... |

3 |
An effective tour construction and improvement procedure for 1148 the traveling salesman problem
- Zweig
- 1995
(Show Context)
Citation Context ... Its advantage is that the technology for solving large Traveling Salesman problems is far advanced, so that near-optimal solutions are very easily obtained. We use a local search method due to Zweig =-=[Z92]-=-, based on an operation called Divide-and-Merge, which rapidly and dependably gives nearoptimal solutions to instances of the Hamming Distance TSP with around one thousand cities. We have found that, ... |

1 |
Andrei Grigoriev and Hans Lehrach. An Algorithm to Detect Chimeric Clones and Random Noise in Genomic Mapping
- Mott
- 1994
(Show Context)
Citation Context ...d in an iterative fashion. Our computational results are summarized in Section 7. vii 2.6 Relationship to Previous Work In the field of physical mapping, simulated annealing has been used by [RML93], =-=[AGL94]-=-, and [ACT93], among others. [RML93] presents a software package used to construct a YAC map of S. pombe. This package uses simulated annealing to minimize a distance measure, d ab = nab \Gammar ab na... |