Assigning confidence scores to homoeologs using fuzzy logic.

Détails

Ressource 1Télécharger: peerj-6231.pdf (4049.92 [Ko])
Etat: Public
Version: Final published version
ID Serval
serval:BIB_D4984F5E8391
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Assigning confidence scores to homoeologs using fuzzy logic.
Périodique
PeerJ
Auteur(s)
Glover N.M., Altenhoff A., Dessimoz C.
ISSN
2167-8359 (Print)
ISSN-L
2167-8359
Statut éditorial
Publié
Date de publication
2019
Peer-reviewed
Oui
Volume
6
Pages
e6231
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: epublish
Résumé
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.
Mots-clé
Comparative genomics, Confidence scores, Fuzzy logic, Homoeology, Polyploidy
Pubmed
Web of science
Open Access
Oui
Création de la notice
31/01/2019 9:09
Dernière modification de la notice
20/08/2019 16:54
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