PedigreeNet: a web-based pedigree viewer for biological databases.
Bioinformatics
; 35(20): 4184-4186, 2019 10 15.
Article
en En
| MEDLINE
| ID: mdl-30903182
ABSTRACT
MOTIVATION Plant breeding aims to improve current germplasm that can tolerate a wide range of biotic and abiotic stresses. To accomplish this goal, breeders rely on developing a deeper understanding of genetic makeup and relationships between plant varieties to make informed plant selections. Although rapid advances in genotyping technology generated a large amount of data for breeders, tools that facilitate pedigree analysis and visualization are scant, leaving breeders to use classical, but inherently limited, hierarchical pedigree diagrams for a handful of plant varieties. To answer this need, we developed a simple web-based tool that can be easily implemented at biological databases, called PedigreeNet, to create and visualize customizable pedigree relationships in a network context, displaying pre- and user-uploaded data. RESULTS:
As a proof-of-concept, we implemented PedigreeNet at the maize model organism database, MaizeGDB. The PedigreeNet viewer at MaizeGDB has a dynamically-generated pedigree network of 4706 maize lines and 5487 relationships that are currently available as both a stand-alone web-based tool and integrated directly on the MaizeGDB Stock Pages. The tool allows the user to apply a number of filters, select or upload their own breeding relationships, center a pedigree network on a plant variety, identify the common ancestor between two varieties, and display the shortest path(s) between two varieties on the pedigree network. The PedigreeNet code layer is written as a JavaScript wrapper around Cytoscape Web. PedigreeNet fills a great need for breeders to have access to an online tool to represent and visually customize pedigree relationships. AVAILABILITY AND IMPLEMENTATION PedigreeNet is accessible at https//www.maizegdb.org/breeders_toolbox. The open source code is publically and freely available at GitHub https//github.com/Maize-Genetics-and-Genomics-Database/PedigreeNet. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Banco de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Zea mays
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2019
Tipo del documento:
Article
País de afiliación:
Estados Unidos