Gilchrist Cameron L M, Booth Thomas J, van Wersch Bram, van Grieken Liana, Medema Marnix H, Chooi Yit-Heng
School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
Bioinformatics Group, Wageningen University, Wageningen 6708PB, The Netherlands.
Bioinform Adv. 2021 Aug 5;1(1):vbab016. doi: 10.1093/bioadv/vbab016. eCollection 2021.
Genes involved in coordinated biological pathways, including metabolism, drug resistance and virulence, are often collocalized as gene clusters. Identifying homologous gene clusters aids in the study of their function and evolution, however, existing tools are limited to searching local sequence databases. Tools for remotely searching public databases are necessary to keep pace with the rapid growth of online genomic data.
Here, we present cblaster, a Python-based tool to rapidly detect collocated genes in local and remote databases. cblaster is easy to use, offering both a command line and a user-friendly graphical user interface. It generates outputs that enable intuitive visualizations of large datasets and can be readily incorporated into larger bioinformatic pipelines. cblaster is a significant update to the comparative genomics toolbox.
cblaster source code and documentation is freely available from GitHub under the MIT license (github.com/gamcil/cblaster).
Supplementary data are available at online.
参与协调生物途径的基因，包括代谢、耐药性和毒力相关基因，通常作为基因簇共定位。识别同源基因簇有助于研究其功能和进化，然而，现有工具仅限于搜索本地序列数据库。随着在线基因组数据的快速增长，需要能够远程搜索公共数据库的工具。
在此，我们展示了cblaster，这是一个基于Python的工具，用于快速检测本地和远程数据库中的共定位基因。cblaster易于使用，提供命令行和用户友好的图形用户界面。它生成的输出能够直观地可视化大型数据集，并且可以很容易地纳入更大的生物信息学流程中。cblaster是比较基因组学工具箱的一次重大更新。
cblaster的源代码和文档可在GitHub上根据MIT许可免费获取（github.com/gamcil/cblaster）。
补充数据可在在线获取。
