Chloroplot : An Online Program for the Versatile Plotting of Organelle Genomes

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dc.contributor.author Zheng, Shuyu
dc.contributor.author Poczai, Peter
dc.contributor.author Hyvönen, Jaakko
dc.contributor.author Tang, Jing
dc.contributor.author Amiryousefi, Ali
dc.date.accessioned 2020-09-28T13:00:02Z
dc.date.available 2020-09-28T13:00:02Z
dc.date.issued 2020-09-25
dc.identifier.citation Zheng , S , Poczai , P , Hyvönen , J , Tang , J & Amiryousefi , A 2020 , ' Chloroplot : An Online Program for the Versatile Plotting of Organelle Genomes ' , Frontiers in Genetics , vol. 11 , 576124 . https://doi.org/10.3389/fgene.2020.576124
dc.identifier.other PURE: 145225089
dc.identifier.other PURE UUID: 4b04afdc-5dc3-46cb-9871-b394b913acec
dc.identifier.other Bibtex: 10.3389/fgene.2020.576124
dc.identifier.other ORCID: /0000-0003-0624-8077/work/82132798
dc.identifier.other WOS: 000576213000001
dc.identifier.other ORCID: /0000-0001-7480-7710/work/99889545
dc.identifier.uri http://hdl.handle.net/10138/319666
dc.description.abstract 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/. en
dc.format.extent 8
dc.language.iso eng
dc.relation.ispartof Frontiers in Genetics
dc.rights cc_by
dc.rights.uri info:eu-repo/semantics/openAccess
dc.subject 1184 Genetics, developmental biology, physiology
dc.subject 11832 Microbiology and virology
dc.subject 113 Computer and information sciences
dc.subject chloroplast genome
dc.subject DNA barcoding
dc.subject endosymbiosis
dc.subject mitochondrial genome
dc.subject photosynthesis
dc.subject Plastomics
dc.subject visualization
dc.subject GENE ORGANIZATION
dc.subject SEQUENCE
dc.subject RESOURCES
dc.subject TOOLS
dc.title Chloroplot : An Online Program for the Versatile Plotting of Organelle Genomes en
dc.type Article
dc.contributor.organization Research Program in Systems Oncology
dc.contributor.organization Faculty of Medicine
dc.contributor.organization University of Helsinki
dc.contributor.organization Research Programs Unit
dc.contributor.organization Botany
dc.contributor.organization Embryophylo
dc.contributor.organization Biosciences
dc.contributor.organization Viikki Plant Science Centre (ViPS)
dc.contributor.organization Finnish Museum of Natural History
dc.contributor.organization Medicum
dc.description.reviewstatus Peer reviewed
dc.relation.doi https://doi.org/10.3389/fgene.2020.576124
dc.relation.issn 1664-8021
dc.rights.accesslevel openAccess
dc.type.version publishedVersion

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