Formulations and hardness of multiple sorting by reversals
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Covering Points of a Digraph with Point-Disjoint Paths and Its Application to Code Optimization
Journal of the ACM (JACM)
The Reconstruction of Doubled Genomes
SIAM Journal on Computing
Genomic distances under deletions and insertions
Theoretical Computer Science - Special papers from: COCOON 2003
Whole Genome Duplications and Contracted Breakpoint Graphs
SIAM Journal on Computing
Heuristics for the gene-duplication problem: a Θ(n) speed-up for the local search
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
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Accurately reconstructing the large-scale gene order in an ancestral genome is a critical step to better understand genome evolution. In this paper, we propose a heuristic algorithm for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a greedy algorithm is used to reconstruct the ancestral orders by connecting genes into contiguous regions based on predicted adjacencies. Computer simulation was used to validate the algorithm. We also applied the method to reconstruct the ancestral genomes of ciliate Paramecium tetraurelia.