scholarly journals REGEN: Ancestral Genome Reconstruction for Bacteria

Genes ◽  
2012 ◽  
Vol 3 (3) ◽  
pp. 423-443 ◽  
Author(s):  
Kuan Yang ◽  
Lenwood S. Heath ◽  
João C. Setubal
Keyword(s):  
Ancestral Genome ◽  
Genome Reconstruction ◽  
Ancestral Genome Reconstruction

scholarly journals Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria

2016 ◽  
Vol 10 (12) ◽  
pp. 2931-2945 ◽  
Author(s):  
Ben O Oyserman ◽  
Francisco Moya ◽  
Christopher E Lawson ◽  
Antonio L Garcia ◽  
Mark Vogt ◽  
...  
Keyword(s):  
Ancestral Genome ◽  
Genome Reconstruction ◽  
Ancestral Genome Reconstruction

scholarly journals Erratum to: Understanding Brassicaceae evolution through ancestral genome reconstruction

2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Florent Murat ◽  
Alexandra Louis ◽  
Florian Maumus ◽  
Alex Armero ◽  
Richard Cook ◽  
...  
Keyword(s):  
Ancestral Genome ◽  
Genome Reconstruction ◽  
Ancestral Genome Reconstruction

A unified ILP framework for core ancestral genome reconstruction problems

2020 ◽  
Vol 36 (10) ◽  
pp. 2993-3003 ◽  
Author(s):  
Pavel Avdeyev ◽  
Nikita Alexeev ◽  
Yongwu Rong ◽  
Max A Alekseyev
Keyword(s):  
Genome Rearrangements ◽  
Supplementary Information ◽  
Whole Genome ◽  
Ancestral Genome ◽  
Genome Reconstruction ◽  
Polynomial Size ◽  
Extensive Evaluation ◽  
Ancestral Genome Reconstruction ◽  
Extant Species ◽  
Genome Duplications

Abstract Motivation One of the key computational problems in comparative genomics is the reconstruction of genomes of ancestral species based on genomes of extant species. Since most dramatic changes in genomic architectures are caused by genome rearrangements, this problem is often posed as minimization of the number of genome rearrangements between extant and ancestral genomes. The basic case of three given genomes is known as the genome median problem. Whole-genome duplications (WGDs) represent yet another type of dramatic evolutionary events and inspire the reconstruction of preduplicated ancestral genomes, referred to as the genome halving problem. Generalization of WGDs to whole-genome multiplication events leads to the genome aliquoting problem. Results In this study, we propose polynomial-size integer linear programming (ILP) formulations for the aforementioned problems. We further obtain such formulations for the restricted and conserved versions of the median and halving problems, which have been recently introduced to improve biological relevance of the solutions. Extensive evaluation of solutions to the different ILP problems demonstrates their good accuracy. Furthermore, since the ILP formulations for the conserved versions have linear size, they provide a novel practical approach to ancestral genome reconstruction, which combines the advantages of homology- and rearrangements-based methods. Availability and implementation Code and data are available in https://github.com/AvdeevPavel/ILP-WGD-reconstructor. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Understanding Brassicaceae evolution through ancestral genome reconstruction

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Florent Murat ◽  
Alexandra Louis ◽  
Florian Maumus ◽  
Alix Armero ◽  
Richard Cooke ◽  
...  
Keyword(s):  
Ancestral Genome ◽  
Genome Reconstruction ◽  
Ancestral Genome Reconstruction
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