article

Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers

Authors:

Zhi-Zhong Chen,

Lusheng WangAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 9, Issue 5

Pages 1515 - 1528

https://doi.org/10.1109/TCBB.2012.79

Published: 01 September 2012 Publication History

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).

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Cited By

Mondal AKordi MBansal M(2020)A Supervised Machine Learning Approach for Distinguishing Between Additive and Replacing Horizontal Gene TransfersProceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics10.1145/3388440.3412428(1-11)Online publication date: 21-Sep-2020
https://dl.acm.org/doi/10.1145/3388440.3412428
Kordi MKundu SBansal MShi XBuck MMa JVeltri P(2019)On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic ReconciliationProceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics10.1145/3307339.3342168(514-523)Online publication date: 4-Sep-2019
https://dl.acm.org/doi/10.1145/3307339.3342168
Haack JZupke ERamirez AWu YLibeskind-Hadas R(2019)Computing the Diameter of the Space of Maximum Parsimony Reconciliations in the Duplication-Transfer-Loss ModelIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2018.284973216:1(14-22)Online publication date: 1-Jan-2019
https://dl.acm.org/doi/10.1109/TCBB.2018.2849732
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cover image IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 9, Issue 5

September 2012

287 pages

ISSN:1545-5963

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IEEE Computer Society Press

Washington, DC, United States

Publication History

Published: 01 September 2012

Published in TCBB Volume 9, Issue 5

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Cited By

Mondal AKordi MBansal M(2020)A Supervised Machine Learning Approach for Distinguishing Between Additive and Replacing Horizontal Gene TransfersProceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics10.1145/3388440.3412428(1-11)Online publication date: 21-Sep-2020
https://dl.acm.org/doi/10.1145/3388440.3412428
Kordi MKundu SBansal MShi XBuck MMa JVeltri P(2019)On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic ReconciliationProceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics10.1145/3307339.3342168(514-523)Online publication date: 4-Sep-2019
https://dl.acm.org/doi/10.1145/3307339.3342168
Haack JZupke ERamirez AWu YLibeskind-Hadas R(2019)Computing the Diameter of the Space of Maximum Parsimony Reconciliations in the Duplication-Transfer-Loss ModelIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2018.284973216:1(14-22)Online publication date: 1-Jan-2019
https://dl.acm.org/doi/10.1109/TCBB.2018.2849732
Zheng YZhang L(2017)Reconciliation With Nonbinary Gene Trees RevisitedJournal of the ACM10.1145/308851264:4(1-28)Online publication date: 17-Aug-2017
https://dl.acm.org/doi/10.1145/3088512
Zheng YZhang L(2014)Reconciliation with Non-binary Gene Trees RevisitedProceedings of the 18th Annual International Conference on Research in Computational Molecular Biology - Volume 839410.1007/978-3-319-05269-4_33(418-432)Online publication date: 2-Apr-2014
https://dl.acm.org/doi/10.1007/978-3-319-05269-4_33
Bansal MAlm EKellis M(2013)Reconciliation revisitedProceedings of the 17th international conference on Research in Computational Molecular Biology10.1007/978-3-642-37195-0_1(1-13)Online publication date: 7-Apr-2013
https://dl.acm.org/doi/10.1007/978-3-642-37195-0_1

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