IRscope: An online program to visualize the junction sites of chloroplast genomes

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dc.contributor University of Helsinki, Biosciences en
dc.contributor University of Helsinki, Finnish Museum of Natural History en
dc.contributor University of Helsinki, Finnish Museum of Natural History en
dc.contributor.author Amiryousefi, Ali
dc.contributor.author Hyvönen, Jaakko Tapani
dc.contributor.author Poczai, Péter
dc.date.accessioned 2019-04-03T21:55:30Z
dc.date.available 2021-10-18T21:46:54Z
dc.date.issued 2018-09-01
dc.identifier.citation Amiryousefi , A , Hyvönen , J T & Poczai , P 2018 , ' IRscope: An online program to visualize the junction sites of chloroplast genomes ' , Bioinformatics , vol. 34 , no. 17 , pp. 3030-3031 . https://doi.org/10.1093/bioinformatics/bty220 en
dc.identifier.issn 1367-4803
dc.identifier.other PURE: 92635272
dc.identifier.other PURE UUID: d2f12db7-1abf-4aa0-9671-ad5329574aaf
dc.identifier.other WOS: 000444317200070
dc.identifier.other Scopus: 85054699270
dc.identifier.uri http://hdl.handle.net/10138/300671
dc.description.abstract Motivation: Genome plotting is performed using a wide range of visualizations tools each with emphasis on a different informative dimension of the genome. These tools can provide a deeper insight into the genomic structure of the organism. Results: Here, we announce a new visualization tool that is specifically designed for chloroplast genomes. It allows the users to depict the genetic architecture of up to ten chloroplast genomes in the vicinity of the sites connecting the inverted repeats to the short and long single copy regions. The software and its dependent libraries are fully coded in R and the reflected plot is scaled up to realistic size of nucleotide base pairs in the vicinity of the junction sites. We introduce a website for easier use of the program and R source code of the software to be used in case of preferences to be changed and integrated into personal pipelines. The input of the program is an annotation GenBank (.gb) file, the accession or GI number of the sequence or a DOGMA output file. The software was tested using over a 100 embryophyte chloroplast genomes and in all cases a reliable output was obtained. en
dc.format.extent 2
dc.language.iso eng
dc.relation.ispartof Bioinformatics
dc.rights en
dc.subject 1182 Biochemistry, cell and molecular biology en
dc.subject DNA en
dc.title IRscope: An online program to visualize the junction sites of chloroplast genomes en
dc.type Article
dc.description.version Peer reviewed
dc.identifier.doi https://doi.org/10.1093/bioinformatics/bty220
dc.type.uri info:eu-repo/semantics/other
dc.type.uri info:eu-repo/semantics/acceptedVersion
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