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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2023
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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) |
format | Online Article Text |
id | pubmed-9852648 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
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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