Ali Amiryousefi1, Jaakko Hyvönen1,2, Peter Poczai2. 1. Organismal Evolutionary Biology Research Program, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre. 2. Finnish Museum of Natural History, University of Helsinki, FI-00014 Helsinki, Finland.
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. Availability and implementation: Source codes and the online suit available at https://irscope.shinyapps.io/irapp/ or https://github.com/Limpfrog/irscope.
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. Availability and implementation: Source codes and the online suit available at https://irscope.shinyapps.io/irapp/ or https://github.com/Limpfrog/irscope.
Authors: Jeison Willy de Souza Magnabosco; Hugo Pacheco de Freitas Fraga; Raquel Santos da Silva; Marcelo Rogalski; Emanuel Maltempi de Souza; Miguel Pedro Guerra; Leila do Nascimento Vieira Journal: Genet Mol Biol Date: 2020-09-11 Impact factor: 1.771
Authors: Virginia M Mwanzia; John M Nzei; Dong-Ying Yan; Peris W Kamau; Jin-Ming Chen; Zhi-Zhong Li Journal: Genetica Date: 2019-10-25 Impact factor: 1.082
Authors: Claudia L Henriquez; Ibrar Ahmed; Monica M Carlsen; Alejandro Zuluaga; Thomas B Croat; Michael R McKain Journal: Planta Date: 2020-02-28 Impact factor: 4.116