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IEEE/ACM Transactions on Computational Biology and Bioinformatics
Article . 2012 . Peer-reviewed
License: IEEE Copyright
Data sources: Crossref
DBLP
Article . 2023
Data sources: DBLP
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Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers

Authors: Zhi-Zhong Chen; Fei Deng; Lusheng Wang 0001;

Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers

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 + 3(k/c)n) 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 + 2.78(k/c)n).

Related Organizations
Keywords

Evolution, Molecular, Gene Transfer, Horizontal, Models, Genetic, Gene Duplication, Algorithms

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
21
Top 10%
Top 10%
Average
bronze