Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
STOC '95 Proceedings of the twenty-seventh annual ACM symposium on Theory of computing
Sorting by reversals is difficult
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Sorting Permutations by Reversals and Eulerian Cycle Decompositions
SIAM Journal on Discrete Mathematics
Approximating discrete collections via local improvements
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Faster and simpler algorithm for sorting signed permutations by reversals
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Estimating true evolutionary distances between genomes
STOC '01 Proceedings of the thirty-third annual ACM symposium on Theory of computing
Sorting Strings by Reversals and by Transpositions
SIAM Journal on Discrete Mathematics
Reconstructing an ancestral genome using minimum segments duplications and reversals
Journal of Computer and System Sciences - Computational biology 2002
Minimum common string partition problem: hardness and approximations
ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
The greedy algorithm for the minimum common string partition problem
ACM Transactions on Algorithms (TALG)
Approximating reversal distance for strings with bounded number of duplicates
Discrete Applied Mathematics
A network flow approach to the minimum common integer partition problem
Theoretical Computer Science
Comparing Genomes with Duplications: A Computational Complexity Point of View
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Approximating the true evolutionary distance between two genomes
Journal of Experimental Algorithmics (JEA)
Expected number of breakpoints after t random reversals in genomes with duplicate genes
Discrete Applied Mathematics
Multichromosomal Genome Median and Halving Problems
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Minimum Common String Partition Parameterized
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
On the minimum common integer partition problem
ACM Transactions on Algorithms (TALG)
Prefix reversals on binary and ternary strings
AB'07 Proceedings of the 2nd international conference on Algebraic biology
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Efficient algorithms for analyzing segmental duplications, deletions, and inversions in genomes
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Quick greedy computation for minimum common string partitions
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Maximizing synteny blocks to identify ancestral homologs
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Alignment with non-overlapping inversions in O(n3)-time
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
On the minimum common integer partition problem
CIAC'06 Proceedings of the 6th Italian conference on Algorithms and Complexity
Better approximations for the minimum common integer partition problem
APPROX'06/RANDOM'06 Proceedings of the 9th international conference on Approximation Algorithms for Combinatorial Optimization Problems, and 10th international conference on Randomization and Computation
Inferring positional homologs with common intervals of sequences
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
How pseudo-boolean programming can help genome rearrangement distance computation
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
Genomes containing duplicates are hard to compare
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
Reversal distance for strings with duplicates: linear time approximation using hitting set
WAOA'06 Proceedings of the 4th international conference on Approximation and Online Algorithms
A parsimony approach to genome-wide ortholog assignment
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Prefix transpositions on binary and ternary strings
Information Processing Letters
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The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics. Existing methods that assign orthologs based on the similarity between DNA or protein sequences may make erroneous assignments when sequence similarity does not clearly delineate the evolutionary relationship among genes of the same families. In this paper, we present a new approach to ortholog assignment that takes into account both sequence similarity and evolutionary events at a genome level, where orthologous genes are assumed to correspond to each other in the most parsimonious evolving scenario under genome rearrangement. First, the problem is formulated as that of computing the signed reversal distance with duplicates between the two genomes of interest. Then, the problem is decomposed into two new optimization problems, called minimum common partition and maximum cycle decomposition, for which efficient heuristic algorithms are given. Following this approach, we have implemented a high-throughput system for assigning orthologs on a genome scale, called SOAR, and tested it on both simulated data and real genome sequence data. Compared to a recent ortholog assignment method based entirely on homology search (called INPARANOID), SOAR shows a marginally better performance in terms of sensitivity on the real data set because it is able to identify several correct orthologous pairs that are missed by INPARANOID. The simulation results demonstrate that SOAR, in general, performs better than the iterated exemplar algorithm in terms of computing the reversal distance and assigning correct orthologs.