PeerJ.: auth.: group Dessimoz

 2019 Jan 11;6:e6231. doi: 10.7717/peerj.6231. eCollection 2019.

Assigning confidence scores to homoeologs using fuzzy logic.

Glover NM1,2,3Altenhoff A1,4Dessimoz C1,2,3,5,6.


In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a “good” homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges.


Comparative genomics; Confidence scores; Fuzzy logic; Homoeology; Polyploidy

PMID: 30648004