Work

Guided Genome Halving:

Year: 2009

Type: book-chapter

Abstract: We present theoretical and practical advances on the Guided Genome Halving problem, a combinatorial optimisation problem which aims at proposing ancestral configurations of extant genomes when one of them has undergone a whole genome duplication. We provide a lower bound on the optimal solution, devise a heuristic algorithm based on subgraph identification, and apply it to yeast gene order data. On some instances, the computation of the bound yields a proof that the obtained solutions are optimal. We analyse a set of optimal solutions, compare them with a manually curated standard ancestor, showing that on yeast data, results coming from different methodologies are largely convergent: the optimal solutions are distant of at most one rearrangement from the reference.

Source: WORLD SCIENTIFIC eBooks

DOI: 10.1142/9789814295291_0004

Authors: HARIS GAVRANOVIĆ, ERIC TANNIER

Institutions: University of Sarajevo, Lyon 1 Université, Centre National de la Recherche Scientifique, Institut national de recherche en sciences et technologies du numérique, Université de Lyon, Laboratoire de Biométrie et Biologie Evolutive, BEAGLE: Artificial Evolution and Computational Biology

Language: English

Topic: Genome Rearrangement Algorithms

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

OpenAlex ID: W1500346027

FWCI: 6.13

Cites: 18

Cited by: 15

Related to: 10