%0 Journal Article
%T A general framework for genome rearrangement with biological constraints
%A Annie Chateau
%A Pijus Simonaitis
%J Archive of "Algorithms for Molecular Biology : AMB".
%D 2019
%R 10.1186/s13015-019-0149-4
%X Eulerian 2-edge-color multi-graphs for genomes A = ( { 3 t , 1 t } , { 1 h , 2 h } , { 2 t , 3 h } ) , ( { 4 t } , { 4 h , 1 t } , { 1 h } ) , B = ( { 1 h , 2 h } , { 2 t , 1 t } ) , ( { 3 t , 2 h } , { 2 t , 1 h } , { 1 t , 3 h } ) , and A ¡ä = ( { 3 t , 2 h } , { 2 t , 1 t } , { 1 h , 2 h } , { 2 t , 3 h } ) , ( { 4 t } , { 4 h , 1 t } , { 1 h } ) . Edges adjacent to a special vertex ¡ã represent the endpoints of linear chromosomes (e.g. black edges { 1 h , ¡ã } and { 4 t , ¡ã } ). Extra edges are added for the missing genes (e.g. the black edge { 2 t , 2 h } and the gray edge { 4 h , 4 t } ), called ghost adjacencies in [15]. In the genomes A and A ¡ä , gene 1 is repeated twice, and the operation transforming A into A ¡ä is an insertion of a gene 2, corresponding to the 2-break G ( A , B ) ¡ú G ( A ¡ä , B ) . A DCJ scenario transforming A ¡ä into the linear genome B includes a deletion of a gene
%K Double cut and join (DCJ)
%K Weighted genome rearrangement
%K Breakpoint graph
%K Graph edit distance
%K Edge switch
%U https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642580/