Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes
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Published on: June 28, 2018
Xi Zhang1, Yining Hu2, David Roy Smith1
1Department of Biology, Western University, London, ON N6A 5B7, Canada.
Abstract:
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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