Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes
Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting t...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-09-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.576124/full |
| _version_ | 1818846762064936960 |
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| author | Shuyu Zheng Peter Poczai Peter Poczai Jaakko Hyvönen Jaakko Hyvönen Jing Tang Ali Amiryousefi |
| author_facet | Shuyu Zheng Peter Poczai Peter Poczai Jaakko Hyvönen Jaakko Hyvönen Jing Tang Ali Amiryousefi |
| author_sort | Shuyu Zheng |
| collection | DOAJ |
| description | Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/. |
| first_indexed | 2024-12-19T05:50:42Z |
| format | Article |
| id | doaj.art-750e7ca510fa449b8129bc42e959d911 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-19T05:50:42Z |
| publishDate | 2020-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-750e7ca510fa449b8129bc42e959d9112022-12-21T20:33:38ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-09-011110.3389/fgene.2020.576124576124Chloroplot: An Online Program for the Versatile Plotting of Organelle GenomesShuyu Zheng0Peter Poczai1Peter Poczai2Jaakko Hyvönen3Jaakko Hyvönen4Jing Tang5Ali Amiryousefi6Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, FinlandFinnish Museum of Natural History (Botany), University of Helsinki, Helsinki, FinlandDepartment of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, FinlandFinnish Museum of Natural History (Botany), University of Helsinki, Helsinki, FinlandDepartment of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, FinlandResearch Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, FinlandResearch Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, FinlandUnderstanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.https://www.frontiersin.org/article/10.3389/fgene.2020.576124/fullchloroplast genomeDNA barcodingendosymbiosismitochondrial genomephotosynthesisPlastomics |
| spellingShingle | Shuyu Zheng Peter Poczai Peter Poczai Jaakko Hyvönen Jaakko Hyvönen Jing Tang Ali Amiryousefi Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes Frontiers in Genetics chloroplast genome DNA barcoding endosymbiosis mitochondrial genome photosynthesis Plastomics |
| title | Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes |
| title_full | Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes |
| title_fullStr | Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes |
| title_full_unstemmed | Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes |
| title_short | Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes |
| title_sort | chloroplot an online program for the versatile plotting of organelle genomes |
| topic | chloroplast genome DNA barcoding endosymbiosis mitochondrial genome photosynthesis Plastomics |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.576124/full |
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