On the Structure of Syntenic Distance (1999) [11 citations — 5 self]
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@ARTICLE{Liben-nowell99onthe,author = {David Liben-nowell},
title = {On the Structure of Syntenic Distance},
journal = {In 10th Annual Symposium on Combinatorial Pattern Matching},
year = {1999},
volume = {8},
pages = {43--56}
}
Years of Citing Articles
Abstract:
Abstract. This paper examines some of the rich structure of the syntenic distance model of evolutionary distance, introduced by Ferretti, Nadeau, and Sanko. The syntenic distance between two genomes is the minimum number of ssions, fusions, and translocations required to transform one into the other, ignoring gene order within chromosomes. We prove that the previously unanalyzed algorithm given by Ferretti et al is a 2-approximation and no better, and that, further, it always outperforms the algorithm presented by DasGupta, Jiang, Kannan, Li, and Sweedyk. We also prove the same results for an improved version of the Ferretti et al algorithm. We then prove a number of properties which give insight into the structure of optimal move sequences. We give instances in which any move sequence working solely within connected components is nearly twice optimal, and a general lower bound based on the spread of genes from each chromosome. We then prove a monotonicity property for the syntenic distance, and bound the diculty of the hardest instance of any given size. We brie y discuss the results of implementing these algorithms and testing them on real synteny data. 1
Citations
| 115 | Genome Rearrangements and Sorting by Reversals – Bafna, Pevzner - 1996 |
| 85 | Sorting by transpositions – Bafna, Pevzner - 1998 |
| 29 | Open combinatorial problems in computational molecular biology – Waterman - 1995 |
| 27 | Original synteny – Ferretti, Nadeau, et al. - 1996 |
| 25 | Genome Rearrangement Problems – Christie - 1999 |
| 17 | On the complexity and approximation of the syntenic distance – DasGupta, Jing, et al. - 1998 |
| 15 | Conserved synteny as a measure of genomic distance – Sankoff, Nadeau - 1996 |
| 10 | Synteny conservation and chromosome rearrangements during mammalian evolution – Ehrlich, Sanko, et al. - 1997 |
| 7 | The syntenic diameter of the space of n-chromosome genomes – Kleinberg, Liben-Nowell - 2000 |
| 7 | Structural Properties and Tractability Results for Linear Synteny – Liben-Nowell, Kleinberg - 2000 |
