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VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features

BACKGROUND: Both the protein domains and transcript structures influence protein functional variation. The genomic location of both protein domains and transcript structural features can be described using the genomic coordinates of their encoded sequences. However, the coordinates of protein domain...

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Autores principales: Wang, Hongwei, Zhang, Xiaotian, Ding, Shuangcheng, Huang, Yujie, Wang, Shengyong, Chen, Huili, Chen, Yuhang, Li, Yuting
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9235191/
https://www.ncbi.nlm.nih.gov/pubmed/35761171
http://dx.doi.org/10.1186/s12864-022-08713-3
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author Wang, Hongwei
Zhang, Xiaotian
Ding, Shuangcheng
Huang, Yujie
Wang, Shengyong
Chen, Huili
Chen, Yuhang
Li, Yuting
author_facet Wang, Hongwei
Zhang, Xiaotian
Ding, Shuangcheng
Huang, Yujie
Wang, Shengyong
Chen, Huili
Chen, Yuhang
Li, Yuting
author_sort Wang, Hongwei
collection PubMed
description BACKGROUND: Both the protein domains and transcript structures influence protein functional variation. The genomic location of both protein domains and transcript structural features can be described using the genomic coordinates of their encoded sequences. However, the coordinates of protein domains and transcriptional features often differ greatly, and it is difficult to view them in combination at the genome-wide level. In this paper, we describe the development of a new tool that allows users to visualize domains and transcript features together, using either built-in or uploaded genome datasets, and export publication-ready figures.  RESULTS: We developed a user-friendly, independent R package and Shiny web application named “VisProDom”. VisProDom consists of a genome-wide database containing entire annotated transcripts merged with annotated protein domains from the Pfam database. The built-in dataset includes 82 files, which merge genome general feature format (GFF) annotations with rpsblast tabular outputs from protein sequence searches in the Pfam database. Multiple genomes can be simultaneously screened for protein domains or transcript names. VisProDom includes step-by-step introductions and clickable elements for ease of use. CONCLUSION: VisProDom can display hundreds of transcripts alongside protein domains and export figures in a publication-ready format. This makes it a valuable tool for molecular evolution and comparative genomics. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08713-3.
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spelling pubmed-92351912022-06-28 VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features Wang, Hongwei Zhang, Xiaotian Ding, Shuangcheng Huang, Yujie Wang, Shengyong Chen, Huili Chen, Yuhang Li, Yuting BMC Genomics Software BACKGROUND: Both the protein domains and transcript structures influence protein functional variation. The genomic location of both protein domains and transcript structural features can be described using the genomic coordinates of their encoded sequences. However, the coordinates of protein domains and transcriptional features often differ greatly, and it is difficult to view them in combination at the genome-wide level. In this paper, we describe the development of a new tool that allows users to visualize domains and transcript features together, using either built-in or uploaded genome datasets, and export publication-ready figures.  RESULTS: We developed a user-friendly, independent R package and Shiny web application named “VisProDom”. VisProDom consists of a genome-wide database containing entire annotated transcripts merged with annotated protein domains from the Pfam database. The built-in dataset includes 82 files, which merge genome general feature format (GFF) annotations with rpsblast tabular outputs from protein sequence searches in the Pfam database. Multiple genomes can be simultaneously screened for protein domains or transcript names. VisProDom includes step-by-step introductions and clickable elements for ease of use. CONCLUSION: VisProDom can display hundreds of transcripts alongside protein domains and export figures in a publication-ready format. This makes it a valuable tool for molecular evolution and comparative genomics. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08713-3. BioMed Central 2022-06-27 /pmc/articles/PMC9235191/ /pubmed/35761171 http://dx.doi.org/10.1186/s12864-022-08713-3 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Wang, Hongwei
Zhang, Xiaotian
Ding, Shuangcheng
Huang, Yujie
Wang, Shengyong
Chen, Huili
Chen, Yuhang
Li, Yuting
VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
title VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
title_full VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
title_fullStr VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
title_full_unstemmed VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
title_short VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
title_sort visprodom: an interactive shiny/r application for displaying protein domains with transcriptional features
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9235191/
https://www.ncbi.nlm.nih.gov/pubmed/35761171
http://dx.doi.org/10.1186/s12864-022-08713-3
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