HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes

Xi Zhang; Yining Hu; Zhenyu Cheng; John M. Archibald

doi:10.1016/j.xpro.2022.102014

HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes

Xi Zhang, Yining Hu, Zhenyu Cheng, John M. Archibald

Medicine

Producción científica: Contribución a una revista › Artículo › revisión exhaustiva

2 Citas (Scopus)

Resumen

Many tools have been developed to measure the degree of similarity between gene duplicates within and between species. Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene sets, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021)¹ and Zhang et al. (2022).²

Idioma original	English
Número de artículo	102014
Publicación	STAR Protocols
Volumen	4
N.º	1
DOI	https://doi.org/10.1016/j.xpro.2022.102014
Estado	Published - mar. 17 2023

Nota bibliográfica

Funding Information:
This work was supported by a Gordon and Betty Moore Foundation grant ( GBMF5782 ) and a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada ( RGPIN-2019- 05058 ) awarded to J.M.A. This work was also supported by a Discovery Grant ( RGPIN 04912 ) from the Natural Sciences and Engineering Research Council of Canada to Z.C. We thank David R. Smith for useful discussion of the manuscript.

Publisher Copyright:
© 2023 The Authors

ASJC Scopus Subject Areas

General Neuroscience
General Biochemistry,Genetics and Molecular Biology
General Immunology and Microbiology

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Journal Article

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title = "HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes",

abstract = "Many tools have been developed to measure the degree of similarity between gene duplicates within and between species. Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene sets, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021)1 and Zhang et al. (2022).2",

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AU - Archibald, John M.

N1 - Funding Information: This work was supported by a Gordon and Betty Moore Foundation grant ( GBMF5782 ) and a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada ( RGPIN-2019- 05058 ) awarded to J.M.A. This work was also supported by a Discovery Grant ( RGPIN 04912 ) from the Natural Sciences and Engineering Research Council of Canada to Z.C. We thank David R. Smith for useful discussion of the manuscript. Publisher Copyright: © 2023 The Authors

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N2 - Many tools have been developed to measure the degree of similarity between gene duplicates within and between species. Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene sets, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021)1 and Zhang et al. (2022).2

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HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes

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