Investigating the complexity of the double distance problems

Algorithms Mol Biol. 2024 Jan 4;19(1):1. doi: 10.1186/s13015-023-00246-y.ABSTRACTBACKGROUND: Two genomes [Formula: see text] and [Formula: see text] over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Denote by [Formula: see text] the number of common families of [Formula: see text] and [Formula: see text]. Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents the relation between the two given genomes as a collection of cycles of even length and paths. Let [Formula: see text] and [Formula: see text] be respectively the numbers of cycles of length i and of paths of length j in the breakpoint graph of genomes [Formula: see text] and [Formula: see text]. Then, the breakpoint distance of [Formula: see text] and [Formula: see text] is equal to [Formula: see text]. Similarly, when the considered rearrangements are those modeled by the double-cut-and-join (DCJ) operation, the rearrangement distance of [Formula: see text] and [Formula: see text] is [Formula: see text], where c is the total number of cycles and [Formula: see text] is the total number of paths of even length.MOTIVATION: The distance formulation is a basic unit for several other combinatorial problems related to genome evolution and ancestral reconstruction, such as median or double distance. Interestingly, both median and double distance problems can be solved in polynomial time for the breakpoint...
Source: Algorithms for Molecular Biology : AMB - Category: Molecular Biology Authors: Source Type: research