Approximating discrete collections via local improvements
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Maximal Strip Recovery Problem with Gaps: Hardness and Approximation Algorithms
ISAAC '09 Proceedings of the 20th International Symposium on Algorithms and Computation
On the parameterized complexity of some optimization problems related to multiple-interval graphs
Theoretical Computer Science
Efficient exact and approximate algorithms for the complement of maximal strip recovery
AAIM'10 Proceedings of the 6th international conference on Algorithmic aspects in information and management
Inapproximability of maximal strip recovery
Theoretical Computer Science
An improved approximation algorithm for the complementary maximal strip recovery problem
Journal of Computer and System Sciences
Exact and approximation algorithms for the complementary maximal strip recovery problem
Journal of Combinatorial Optimization
| Hi-index | 5.23 |
An essential task in comparative genomics is to decompose two or more genomes into synteny blocks that are segments of chromosomes with similar contents. Given a set of d genomic maps each containing the same n markers without duplicates, the problem Maximal Strip Recovery (MSR) aims at finding a decomposition of the genomic maps into synteny blocks (strips) of the maximum total length @?, by deleting the minimum number k=n-@? of markers which are probably noise and ambiguities. In this paper, we present a collection of new or improved FPT and approximation algorithms for MSR and its variants. Our main results include a 2^O^(^d^@d^@?^)poly(nd) time FPT algorithm for @d-gap-MSR-d, a 2.36^kpoly(nd) time FPT algorithm for both CMSR-d and @d-gap-CMSR-d, and a (d+1.5)-approximation algorithm for both CMSR-d and @d-gap-CMSR-d.