Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes

Although gene duplications have been documented in many species, the precise numbers of highly similar duplicated genes (HSDs) in eukaryotic nuclear genomes remain largely unknown and can be time-consuming to explore. We developed HSDFinder to identify, categorize, and visualize HSDs in eukaryotic n...

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Detalles Bibliográficos
Autores principales: Zhang, Xi, Hu, Yining, Smith, David Roy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8243146/
https://www.ncbi.nlm.nih.gov/pubmed/34223195
http://dx.doi.org/10.1016/j.xpro.2021.100619
Descripción
Sumario:Although gene duplications have been documented in many species, the precise numbers of highly similar duplicated genes (HSDs) in eukaryotic nuclear genomes remain largely unknown and can be time-consuming to explore. We developed HSDFinder to identify, categorize, and visualize HSDs in eukaryotic nuclear genomes using protein family domains and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In contrast to existing tools, HSDFinder allows users to compare HSDs among different species and visualize results in different KEGG pathway functional categories via heatmap plotting. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021).

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