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Issue No.05 - Sept.-Oct. (2012 vol.9)
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
ABSTRACT
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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