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

Xi Zhang; Yining Hu; David Roy Smith

doi:10.1016/j.xpro.2021.100619

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

STAR Protoc. 2021 Jun 23;2(3):100619. doi: 10.1016/j.xpro.2021.100619. eCollection 2021 Sep 17.

Authors

Xi Zhang¹, Yining Hu², David Roy Smith¹

Affiliations

¹ Department of Biology, Western University, London, ON N6A 5B7, Canada.
² Department of Computer Science, 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).

Keywords: Bioinformatics; Genomics; Sequence analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods
Eukaryotic Cells
Gene Duplication*
Genome*
Internet
Molecular Sequence Annotation