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

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http://hdl.handle.net/10138/319666

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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

Titel: Chloroplot : An Online Program for the Versatile Plotting of Organelle Genomes
Författare: Zheng, Shuyu; Poczai, Peter; Hyvönen, Jaakko; Tang, Jing; Amiryousefi, Ali
Upphovmannens organisation: Research Program in Systems Oncology
Faculty of Medicine
University of Helsinki
Research Programs Unit
Botany
Embryophylo
Biosciences
Viikki Plant Science Centre (ViPS)
Finnish Museum of Natural History
Medicum
Datum: 2020-09-25
Språk: eng
Sidantal: 8
Tillhör serie: Frontiers in Genetics
ISSN: 1664-8021
DOI: https://doi.org/10.3389/fgene.2020.576124
Permanenta länken (URI): http://hdl.handle.net/10138/319666
Abstrakt: 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/.
Subject: 1184 Genetics, developmental biology, physiology
11832 Microbiology and virology
113 Computer and information sciences
chloroplast genome
DNA barcoding
endosymbiosis
mitochondrial genome
photosynthesis
Plastomics
visualization
GENE ORGANIZATION
SEQUENCE
RESOURCES
TOOLS
Referentgranskad: Ja
Licens: cc_by
Användningsbegränsning: openAccess
Parallelpublicerad version: publishedVersion


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