Reversal distance for strings with duplicates: Linear time approximation using hitting set
In the last decade there has been an ongoing interest in string comparison problems; to a
large extend the interest was stimulated by genome rearrangement problems in …
large extend the interest was stimulated by genome rearrangement problems in …
Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions
The rearrangement distance is a method to compare genomes of different species. Such
distance is the number of rearrangement events necessary to transform one genome into …
distance is the number of rearrangement events necessary to transform one genome into …
Minimum common string partition revisited
Abstract Minimum Common String Partition (MCSP) has drawn much attention due to its
application in genome rearrangement. In this paper, we investigate three variants of MCSP …
application in genome rearrangement. In this paper, we investigate three variants of MCSP …
[HTML][HTML] Solving the maximum duo-preservation string mapping problem with linear programming
W Chen, Z Chen, NF Samatova, L Peng, J Wang… - Theoretical Computer …, 2014 - Elsevier
In this paper, we introduce the maximum duo-preservation string mapping problem (MPSM),
which is complementary to the minimum common string partition problem (MCSP). When …
which is complementary to the minimum common string partition problem (MCSP). When …
A pseudo-boolean framework for computing rearrangement distances between genomes with duplicates
S Angibaud, G Fertin, I Rusu… - Journal of Computational …, 2007 - liebertpub.com
Computing genomic distances between whole genomes is a fundamental problem in
comparative genomics. Recent researches have resulted in different genomic distance …
comparative genomics. Recent researches have resulted in different genomic distance …
Improved approximation for the maximum duo-preservation string mapping problem
In this paper we present improved approximation results for the max duo-preservation string
mapping problem (MPSM) introduced in [Chen et al., Theoretical Computer Science, 2014] …
mapping problem (MPSM) introduced in [Chen et al., Theoretical Computer Science, 2014] …
The edge-preservation similarity for comparing rooted, unordered, node-labeled trees
Rooted trees are ubiquitous data structures which are used to model hierarchical objects
from a plethora of different application domains. For various downstream analysis tasks …
from a plethora of different application domains. For various downstream analysis tasks …
A 7/2-approximation algorithm for the maximum duo-preservation string mapping problem
This paper presents a simple 7/2-approximation algorithm for the Maximum Duo-
Preservation String Mapping (MPSM) problem. This problem is complementary to the …
Preservation String Mapping (MPSM) problem. This problem is complementary to the …
Partition Based Algorithms for Rearrangement Distances with Flexible Intergenic Regions
G Siqueira, AO Alexandrino, AR Oliveira… - IEEE/ACM …, 2024 - ieeexplore.ieee.org
Genome Rearrangement distance problems are used in Computational Biology to estimate
the evolutionary distance between genomes. These problems consist of minimizing the …
the evolutionary distance between genomes. These problems consist of minimizing the …
Further improvement in approximating the maximum duo-preservation string mapping problem
B Brubach - International Workshop on Algorithms in Bioinformatics, 2016 - Springer
We present an improved approximation for the Maximum Duo-Preservation String Mapping
Problem (MPSM). This problem was introduced in 7 as the complement to the well-studied …
Problem (MPSM). This problem was introduced in 7 as the complement to the well-studied …