title: DUPCAR: reconstructing contiguous ancestral regions with duplications.
abstract: 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, called DUPCAR, 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 chromosome X of placental mammals and the ancestral genomes of the ciliate Paramecium tetraurelia.
authors.affiliation: Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. jianma@soe.ucsc.edu
authors.forename: Jian
authors.initials: J
authors.lastname: Ma
authors.forename: Aakrosh
authors.initials: A
authors.lastname: Ratan
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Raney
authors.forename: Bernard B
authors.initials: BB
authors.lastname: Suh
authors.forename: Louxin
authors.initials: L
authors.lastname: Zhang
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.forename: David
authors.initials: D
authors.lastname: Haussler
mesh_terms: D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D019143:Evolution, Molecular; D020440:Gene Duplication; D016678:Genome; D006801:Humans; D008957:Models, Genetic; D016805:Paramecium tetraurelia / Q000235:genetics; D010802:Phylogeny
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