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

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

Summary: 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 euk...

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Bibliographic Details
Main Authors: Xi Zhang, Yining Hu, David Roy Smith
Format: Article
Language:English
Published: Elsevier 2021-09-01
Series:STAR Protocols
Subjects:
Bioinformatics
Genomics
Sequence analysis
Online Access:http://www.sciencedirect.com/science/article/pii/S2666166721003269
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spelling doaj-5aecd189cab54d57818aed2b312b29612021-09-19T04:59:55ZengElsevierSTAR Protocols2666-16672021-09-0123100619Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomesXi Zhang0Yining Hu1David Roy Smith2Department of Biology, Western University, London, ON N6A 5B7, Canada; Corresponding authorDepartment of Computer Science, Western University, London, ON N6A 5B7, CanadaDepartment of Biology, Western University, London, ON N6A 5B7, Canada; Corresponding authorSummary: 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).http://www.sciencedirect.com/science/article/pii/S2666166721003269BioinformaticsGenomicsSequence analysis
collection DOAJ
language English
format Article
sources DOAJ
author Xi Zhang
Yining Hu
David Roy Smith
spellingShingle Xi Zhang
Yining Hu
David Roy Smith
Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes
STAR Protocols
Bioinformatics
Genomics
Sequence analysis
author_facet Xi Zhang
Yining Hu
David Roy Smith
author_sort Xi Zhang
title Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes
title_short Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes
title_full Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes
title_fullStr Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes
title_full_unstemmed Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes
title_sort protocol for hsdfinder: identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes
publisher Elsevier
series STAR Protocols
issn 2666-1667
publishDate 2021-09-01
description Summary: 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).
topic Bioinformatics
Genomics
Sequence analysis
url http://www.sciencedirect.com/science/article/pii/S2666166721003269
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AT yininghu protocolforhsdfinderidentifyingannotatingcategorizingandvisualizingduplicatedgenesineukaryoticgenomes
AT davidroysmith protocolforhsdfinderidentifyingannotatingcategorizingandvisualizingduplicatedgenesineukaryoticgenomes
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