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

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...

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Detalles Bibliográficos
Autores principales: Zhang, Xi, Hu, Yining, Cheng, Zhenyu, Archibald, John M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9852648/
https://www.ncbi.nlm.nih.gov/pubmed/36633953
http://dx.doi.org/10.1016/j.xpro.2022.102014
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author Zhang, Xi
Hu, Yining
Cheng, Zhenyu
Archibald, John M.
author_facet Zhang, Xi
Hu, Yining
Cheng, Zhenyu
Archibald, John M.
author_sort Zhang, Xi
collection PubMed
description 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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spelling pubmed-98526482023-01-21 HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes Zhang, Xi Hu, Yining Cheng, Zhenyu Archibald, John M. STAR Protoc Protocol 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) Elsevier 2023-01-11 /pmc/articles/PMC9852648/ /pubmed/36633953 http://dx.doi.org/10.1016/j.xpro.2022.102014 Text en © 2023 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Zhang, Xi
Hu, Yining
Cheng, Zhenyu
Archibald, John M.
HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes
title HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes
title_full HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes
title_fullStr HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes
title_full_unstemmed HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes
title_short HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes
title_sort hsdecipher: a pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9852648/
https://www.ncbi.nlm.nih.gov/pubmed/36633953
http://dx.doi.org/10.1016/j.xpro.2022.102014
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