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Assigning confidence scores to homoeologs using fuzzy logic

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)....

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Detalles Bibliográficos
Autores principales: Glover, Natasha M., Altenhoff, Adrian, Dessimoz, Christophe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330999/
https://www.ncbi.nlm.nih.gov/pubmed/30648004
http://dx.doi.org/10.7717/peerj.6231
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author Glover, Natasha M.
Altenhoff, Adrian
Dessimoz, Christophe
author_facet Glover, Natasha M.
Altenhoff, Adrian
Dessimoz, Christophe
author_sort Glover, Natasha M.
collection PubMed
description 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.
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spelling pubmed-63309992019-01-15 Assigning confidence scores to homoeologs using fuzzy logic Glover, Natasha M. Altenhoff, Adrian Dessimoz, Christophe PeerJ Bioinformatics 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. PeerJ Inc. 2019-01-11 /pmc/articles/PMC6330999/ /pubmed/30648004 http://dx.doi.org/10.7717/peerj.6231 Text en © 2019 Glover et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Glover, Natasha M.
Altenhoff, Adrian
Dessimoz, Christophe
Assigning confidence scores to homoeologs using fuzzy logic
title Assigning confidence scores to homoeologs using fuzzy logic
title_full Assigning confidence scores to homoeologs using fuzzy logic
title_fullStr Assigning confidence scores to homoeologs using fuzzy logic
title_full_unstemmed Assigning confidence scores to homoeologs using fuzzy logic
title_short Assigning confidence scores to homoeologs using fuzzy logic
title_sort assigning confidence scores to homoeologs using fuzzy logic
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330999/
https://www.ncbi.nlm.nih.gov/pubmed/30648004
http://dx.doi.org/10.7717/peerj.6231
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