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Approximating the double-cut-and-join distance between unsigned genomes

In this paper we study the problem of sorting unsigned genomes by double-cut-and-join operations, where genomes allow a mix of linear and circular chromosomes to be present. First, we formulate an equivalent optimization problem, called maximum cycle/path decomposition, which is aimed at finding a l...

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Detalles Bibliográficos
Autores principales: Chen, Xin, Sun, Ruimin, Yu, Jiadong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3283313/
https://www.ncbi.nlm.nih.gov/pubmed/22151948
http://dx.doi.org/10.1186/1471-2105-12-S9-S17
Descripción
Sumario:In this paper we study the problem of sorting unsigned genomes by double-cut-and-join operations, where genomes allow a mix of linear and circular chromosomes to be present. First, we formulate an equivalent optimization problem, called maximum cycle/path decomposition, which is aimed at finding a largest collection of edge-disjoint cycles/AA-paths/AB-paths in a breakpoint graph. Then, we show that the problem of finding a largest collection of edge-disjoint cycles/AA-paths/AB-paths of length no more than l can be reduced to the well-known degree-bounded k-set packing problem with k = 2l. Finally, a polynomial-time approximation algorithm for the problem of sorting unsigned genomes by double-cut-and-join operations is devised, which achieves the approximation ratio [Image: see text] for any positive ε. For the restricted variation where each genome contains only one linear chromosome, the approximation ratio can be further improved to [Image: see text]