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Assigning confidence scores to homoeologs using fuzzy logic

Glover, NM; Altenhoff, A; Dessimoz, C; (2019) Assigning confidence scores to homoeologs using fuzzy logic. PeerJ , 6 , Article e6231. 10.7717/peerj.6231. Green open access

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Abstract

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.

Type: Article
Title: Assigning confidence scores to homoeologs using fuzzy logic
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.7717/peerj.6231
Publisher version: https://doi.org/10.7717/peerj.6231
Language: English
Additional information: © 2019 Glover et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 International (https://creativecommons.org/licenses/by/4.0/).
Keywords: Homoeology, Fuzzy logic, Polyploidy, Confidence scores, Comparative genomics
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10066388
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