The ultimate interval graph recognition algorithm?
Proceedings of the ninth annual ACM-SIAM symposium on Discrete algorithms
Efficient algorithms for multichromosomal genome rearrangements
Journal of Computer and System Sciences - Computational biology 2002
A new algorithm for the maximum-weight clique problem
Nordic Journal of Computing
A fast algorithm for the maximum clique problem
Discrete Applied Mathematics - Sixth Twente Workshop on Graphs and Combinatorial Optimization
Barnacle: an assembly algorithm for clone-based sequences of whole genomes
Barnacle: an assembly algorithm for clone-based sequences of whole genomes
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On Recovering Syntenic Blocks from Comparative Maps
COCOA 2008 Proceedings of the 2nd international conference on Combinatorial Optimization and Applications
Approximability and Fixed-Parameter Tractability for the Exemplar Genomic Distance Problems
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
On the Tractability of Maximal Strip Recovery
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
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
Tractability and approximability of maximal strip recovery
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
An improved approximation algorithm for the complementary maximal strip recovery problem
FAW-AAIM'11 Proceedings of the 5th joint international frontiers in algorithmics, and 7th international conference on Algorithmic aspects in information and management
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
A linear kernel for the complementary maximal strip recovery problem
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
Maximal strip recovery problem with gaps: Hardness and approximation algorithms
Journal of Discrete Algorithms
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In comparing genomic maps, we try to distinguish mapping errors and incorrectly resolved paralogies from genuine rearrangements of the genomes. This can be formulated as a Maximum Weight Independent Set (MWIS) search, where vertices are potential strips of markers syntenic on both genomes, and edges join conflicting strips, in order to extract the subset of compatible strips that accounts for the largest proportion of the data. This technique is computationally hard. We introduce biologically meaningful constraints on the strips, reducing the number of vertices for the MWIS analysis and provoking a decomposition of the graph into more tractable components. New improvements to existing MWIS algorithms greatly improve running time, especially when the strip conflicts define an interval graph structure. A validation of solutions through genome rearrangement analysis enables us to identify the most realistic solution. We apply this to the comparison of the rice and sorghum genomes.