Organismal Evolutionary Biology Research Program, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre.
Finnish Museum of Natural History, University of Helsinki, FI-00014 Helsinki, Finland.
Bioinformatics. 2018 Sep 1;34(17):3030-3031. doi: 10.1093/bioinformatics/bty220.
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.
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.
Source codes and the online suit available at https://irscope.shinyapps.io/irapp/ or https://github.com/Limpfrog/irscope.
基因组绘图是使用各种可视化工具完成的，每种工具都侧重于基因组的不同信息维度。这些工具可以更深入地了解生物体的基因组结构。
在这里，我们宣布了一个专门为叶绿体基因组设计的新可视化工具。它允许用户在连接反向重复与短和长单拷贝区域的位点附近描绘多达十个叶绿体基因组的遗传结构。该软件及其相关库完全用 R 编写，反映的图谱按比例放大到连接位点附近核苷酸碱基对的实际大小。我们引入了一个网站，以便更轻松地使用该程序，以及 R 源代码，以便在需要更改和集成到个人管道时使用。该程序的输入是一个注释 GenBank（.gb）文件、序列的访问号或 GI 号或 DOGMA 输出文件。该软件已使用 100 多个胚胎植物叶绿体基因组进行了测试，在所有情况下都获得了可靠的输出。
源代码和在线套件可在 https://irscope.shinyapps.io/irapp/ 或 https://github.com/Limpfrog/irscope 上获得。
