David
Liben-Nowell
instances
maximum possible number
genome
2000
non-trivial performance guarantees
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.
polynomial time algorithm
false
fission
main contribution
structural properties
syntenic distance
2022-05-20T07:44
results
en
efficient approximation algorithm
https://scigraph.springernature.com/explorer/license/
form
algorithm
synteny
chapter
paper
literature
scheduling problem
non-trivial class
performance guarantees
2000-01-01
time algorithm
fusion
contribution
distance
research literature
guarantees
https://doi.org/10.1007/3-540-45123-4_22
novel connection
class
reduction
properties
translocation
approximation algorithm
possible number
useful properties
tractability results
chapters
Structural Properties and Tractability Results for Linear Synteny
model
problem
minimum number
248-263
operations research literature
first polynomial-time algorithm
questions
species
number
connection
Computation Theory and Mathematics
pub.1005695677
dimensions_id
Jon
Kleinberg
doi
10.1007/3-540-45123-4_22
Department of Computer Science, Cornell University, 14853, Ithaca, NY, USA
Department of Computer Science, Cornell University, 14853, Ithaca, NY, USA
Information and Computing Sciences
Raffaele
Giancarlo
Springer Nature - SN SciGraph project
Springer Nature
978-3-540-67633-1
978-3-540-45123-5
Combinatorial Pattern Matching
David
Sankoff