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Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers
Sept.-Oct. 2012 (vol. 9 no. 5)
pp. 1515-1528
Zhi-Zhong Chen, Div. of Inf. Syst. Design, Tokyo Denki Univ., Saitama, Japan
Fei Deng, Dept. of Comput. Sci., City Univ. of Hong Kong, Kowloon, China
Lusheng Wang, Dept. of Comput. Sci., City Univ. of Hong Kong, Kowloon, China
We give a fixed-parameter algorithm for the problem of enumerating all minimum-cost LCA-reconciliations involving gene duplications, gene losses, and lateral gene transfers (LGTs) for a given species tree S and a given gene tree G. Our algorithm can work for the weighted version of the problem, where the costs of a gene duplication, a gene loss, and an LGT are left to the user's discretion. The algorithm runs in O(m + 3k=cn) time, where m is the number of vertices in S, n is the number of vertices in G, c is the smaller between a gene duplication cost and an LGT cost, and k is the minimum cost of an LCA-reconciliation between S and G. The time complexity is indeed better if the cost of a gene loss is greater than 0. In particular, when the cost of a gene loss is at least 0:614c, the running time of the algorithm is O(m + 2:78k=cn).
Index Terms:
genetics,biology computing,user discretion,lateral gene transfers,fixed-parameter algorithm,minimum-cost LCA-reconciliations,gene duplications,gene losses,Vegetation,Law,Algorithm design and analysis,Computational biology,Bioinformatics,Biological system modeling,fixed-parameter algorithms.,Phylogenetic trees,reconciliations
Citation:
Zhi-Zhong Chen, Fei Deng, Lusheng Wang, "Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 5, pp. 1515-1528, Sept.-Oct. 2012, doi:10.1109/TCBB.2012.79
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