The potential of family-free rearrangements towards gene orthology inference

Abstract

Recently, we proposed an efficient ILP formulation [Rubert DP, Martinez FV, Braga MDV, Natural family-free genomic distance, Algorithms Mol Biol 16:4, 2021] for exactly computing the rearrangement distance of two genomes in a family-free setting. In such a setting, neither prior classification of genes into families, nor further restrictions on the genomes are imposed. Given two genomes, the mentioned ILP computes an optimal matching of the genes taking into account simultaneously local mutations, given by gene similarities, and large-scale genome rearrangements. Here, we explore the potential of using this ILP for inferring groups of orthologs across several species. More precisely, given a set of genomes, our method first computes all pairwise optimal gene matchings, which are then integrated into gene families in the second step. Our approach is implemented into a pipeline incorporating the pre-computation of gene similarities. It can be downloaded from gitlab.ub.uni-bielefeld.de/gi/FFGC. We obtained promising results with experiments on both simulated and real data.