Please use this identifier to cite or link to this item: https://doi.org/10.1089/cmb.2008.0069
Title: DUPCAR: Reconstructing contiguous ancestral regions with duplications
Authors: Ma, J.
Ratan, A.
Raney, B.J.
Suh, B.B.
Zhang, L. 
Miller, W.
Haussler, D.
Keywords: Contiguous ancestral region
Duplication
Gene-order reconstruction
Genome rearrangement
Isometric reconciliation
Issue Date: 1-Oct-2008
Citation: Ma, J., Ratan, A., Raney, B.J., Suh, B.B., Zhang, L., Miller, W., Haussler, D. (2008-10-01). DUPCAR: Reconstructing contiguous ancestral regions with duplications. Journal of Computational Biology 15 (8) : 1007-1027. ScholarBank@NUS Repository. https://doi.org/10.1089/cmb.2008.0069
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. © Mary Ann Liebert, Inc. 2008.
Source Title: Journal of Computational Biology
URI: http://scholarbank.nus.edu.sg/handle/10635/104559
ISSN: 10665277
DOI: 10.1089/cmb.2008.0069
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