Efficient gene orthology inference via large-scale rearrangements.

ABSTRACT:

Background

Recently we developed a gene orthology inference tool based on genome rearrangements (Journal of Bioinformatics and Computational Biology 19:6, 2021). Given a set of genomes our method first computes all pairwise gene similarities. Then it runs pairwise ILP comparisons to compute optimal gene matchings, which minimize, by taking the similarities into account, the weighted rearrangement distance between the analyzed genomes (a problem that is NP-hard). The gene matchings are then integrated into gene families in the final step. The mentioned ILP includes an optimal capping that connects each end of a linear segment of one genome to an end of a linear segment in the other genome, producing an exponential increase of the search space.

Results

In this work, we design

SUBMITTER: Rubert DP 

PROVIDER: S-EPMC10540461 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature