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 domains...
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Autor*in:	Wang, Hongwei [verfasserIn] Zhang, Xiaotian Ding, Shuangcheng Huang, Yujie Wang, Shengyong Chen, Huili Chen, Yuhang Li, Yuting

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	Protein domain Transcript structure R package Shiny application Visualization

Anmerkung:	© The Author(s) 2022

Übergeordnetes Werk:	Enthalten in: BMC genomics - London : BioMed Central, 2000, 23(2022), 1 vom: 27. Juni
Übergeordnetes Werk:	volume:23 ; year:2022 ; number:1 ; day:27 ; month:06

Links:	Volltext

DOI / URN:	10.1186/s12864-022-08713-3

Katalog-ID:	SPR050813722

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520			\|a 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.
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700	1		\|a Li, Yuting \|4 aut
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Indexfelder

author_variant	h w hw x z xz s d sd y h yh s w sw h c hc y c yc y l yl
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allfields	10.1186/s12864-022-08713-3 doi (DE-627)SPR050813722 (SPR)s12864-022-08713-3-e DE-627 ger DE-627 rakwb eng Wang, Hongwei verfasserin (orcid)0000-0001-6005-9352 aut VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 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. Protein domain (dpeaa)DE-He213 Transcript structure (dpeaa)DE-He213 R package (dpeaa)DE-He213 Shiny application (dpeaa)DE-He213 Visualization (dpeaa)DE-He213 Zhang, Xiaotian aut Ding, Shuangcheng aut Huang, Yujie aut Wang, Shengyong aut Chen, Huili aut Chen, Yuhang aut Li, Yuting aut Enthalten in BMC genomics London : BioMed Central, 2000 23(2022), 1 vom: 27. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:23 year:2022 number:1 day:27 month:06 https://dx.doi.org/10.1186/s12864-022-08713-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 27 06
spelling	10.1186/s12864-022-08713-3 doi (DE-627)SPR050813722 (SPR)s12864-022-08713-3-e DE-627 ger DE-627 rakwb eng Wang, Hongwei verfasserin (orcid)0000-0001-6005-9352 aut VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 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. Protein domain (dpeaa)DE-He213 Transcript structure (dpeaa)DE-He213 R package (dpeaa)DE-He213 Shiny application (dpeaa)DE-He213 Visualization (dpeaa)DE-He213 Zhang, Xiaotian aut Ding, Shuangcheng aut Huang, Yujie aut Wang, Shengyong aut Chen, Huili aut Chen, Yuhang aut Li, Yuting aut Enthalten in BMC genomics London : BioMed Central, 2000 23(2022), 1 vom: 27. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:23 year:2022 number:1 day:27 month:06 https://dx.doi.org/10.1186/s12864-022-08713-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 27 06
allfields_unstemmed	10.1186/s12864-022-08713-3 doi (DE-627)SPR050813722 (SPR)s12864-022-08713-3-e DE-627 ger DE-627 rakwb eng Wang, Hongwei verfasserin (orcid)0000-0001-6005-9352 aut VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 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. Protein domain (dpeaa)DE-He213 Transcript structure (dpeaa)DE-He213 R package (dpeaa)DE-He213 Shiny application (dpeaa)DE-He213 Visualization (dpeaa)DE-He213 Zhang, Xiaotian aut Ding, Shuangcheng aut Huang, Yujie aut Wang, Shengyong aut Chen, Huili aut Chen, Yuhang aut Li, Yuting aut Enthalten in BMC genomics London : BioMed Central, 2000 23(2022), 1 vom: 27. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:23 year:2022 number:1 day:27 month:06 https://dx.doi.org/10.1186/s12864-022-08713-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 27 06
allfieldsGer	10.1186/s12864-022-08713-3 doi (DE-627)SPR050813722 (SPR)s12864-022-08713-3-e DE-627 ger DE-627 rakwb eng Wang, Hongwei verfasserin (orcid)0000-0001-6005-9352 aut VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 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. Protein domain (dpeaa)DE-He213 Transcript structure (dpeaa)DE-He213 R package (dpeaa)DE-He213 Shiny application (dpeaa)DE-He213 Visualization (dpeaa)DE-He213 Zhang, Xiaotian aut Ding, Shuangcheng aut Huang, Yujie aut Wang, Shengyong aut Chen, Huili aut Chen, Yuhang aut Li, Yuting aut Enthalten in BMC genomics London : BioMed Central, 2000 23(2022), 1 vom: 27. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:23 year:2022 number:1 day:27 month:06 https://dx.doi.org/10.1186/s12864-022-08713-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 27 06
allfieldsSound	10.1186/s12864-022-08713-3 doi (DE-627)SPR050813722 (SPR)s12864-022-08713-3-e DE-627 ger DE-627 rakwb eng Wang, Hongwei verfasserin (orcid)0000-0001-6005-9352 aut VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 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. Protein domain (dpeaa)DE-He213 Transcript structure (dpeaa)DE-He213 R package (dpeaa)DE-He213 Shiny application (dpeaa)DE-He213 Visualization (dpeaa)DE-He213 Zhang, Xiaotian aut Ding, Shuangcheng aut Huang, Yujie aut Wang, Shengyong aut Chen, Huili aut Chen, Yuhang aut Li, Yuting aut Enthalten in BMC genomics London : BioMed Central, 2000 23(2022), 1 vom: 27. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:23 year:2022 number:1 day:27 month:06 https://dx.doi.org/10.1186/s12864-022-08713-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 27 06
language	English
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authorswithroles_txt_mv	Wang, Hongwei @@aut@@ Zhang, Xiaotian @@aut@@ Ding, Shuangcheng @@aut@@ Huang, Yujie @@aut@@ Wang, Shengyong @@aut@@ Chen, Huili @@aut@@ Chen, Yuhang @@aut@@ Li, Yuting @@aut@@
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author	Wang, Hongwei
spellingShingle	Wang, Hongwei misc Protein domain misc Transcript structure misc R package misc Shiny application misc Visualization VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
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topic_title	VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features Protein domain (dpeaa)DE-He213 Transcript structure (dpeaa)DE-He213 R package (dpeaa)DE-He213 Shiny application (dpeaa)DE-He213 Visualization (dpeaa)DE-He213
topic	misc Protein domain misc Transcript structure misc R package misc Shiny application misc Visualization
topic_unstemmed	misc Protein domain misc Transcript structure misc R package misc Shiny application misc Visualization
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title	VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
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title_full	VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
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title_sort	visprodom: an interactive shiny/r application for displaying protein domains with transcriptional features
title_auth	VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
abstract	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. © The Author(s) 2022
abstractGer	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. © The Author(s) 2022
abstract_unstemmed	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. © The Author(s) 2022
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title_short	VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
url	https://dx.doi.org/10.1186/s12864-022-08713-3
remote_bool	true
author2	Zhang, Xiaotian Ding, Shuangcheng Huang, Yujie Wang, Shengyong Chen, Huili Chen, Yuhang Li, Yuting
author2Str	Zhang, Xiaotian Ding, Shuangcheng Huang, Yujie Wang, Shengyong Chen, Huili Chen, Yuhang Li, Yuting
ppnlink	326644954
mediatype_str_mv	c
isOA_txt	true
hochschulschrift_bool	false
doi_str	10.1186/s12864-022-08713-3
up_date	2024-07-03T17:56:37.561Z
_version_	1803581545586360320
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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. 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VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features

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