Conserved synteny as a measure of genomic distance
Discrete Applied Mathematics - Special volume on computational molecular biology
Sorting by reversals is difficult
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
SIAM Journal on Discrete Mathematics
On the complexity and approximation of syntenic distance
Discrete Applied Mathematics - Special volume on computational molecular biology DAM-CMB series volume 2
A 3/2-approximation algorithm for sorting by reversals
Proceedings of the ninth annual ACM-SIAM symposium on Discrete algorithms
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Genome Rearrangements and Sorting by Reversals
SIAM Journal on Computing
CPM '96 Proceedings of the 7th Annual Symposium on Combinatorial Pattern Matching
On the Structure of Syntenic Distance
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
Hi-index | 0.00 |
The syntenic distance between two species is the minimum number of fusions, fissions, and translocations required to transform one genome into the other. The linear syntenic distance, a restricted form of this model, has been shown to be close to the syntenic distance. Both models are computationally difficult to compute and have resisted efficient approximation algorithms with non-trivial performance guarantees. In this paper, we prove that many useful properties of syntenic distance carry over to linear syntenic distance. We also give a reduction from the general linear synteny problem to the question of whether a given instance can be solved using the maximum possible number of translocations. Our main contribution is an algorithm exactly computing linear syntenic distance in nested instances of the problem. This is the first polynomial time algorithm exactly solving linear synteny for a non-trivial class of instances. It is based on a novel connection between the syntenic distance and a scheduling problem that has been studied in the operations research literature.