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