cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters

被引：133

作者：

Gilchrist, Cameron L. M. ^{[1
]}

Booth, Thomas J. ^{[1
]}

van Wersch, Bram ^{[2
]}

van Grieken, Liana ^{[2
]}

Medema, Marnix H. ^{[2
]}

Chooi, Yit-Heng ^{[1
]}

机构：

[1] Univ Western Australia, Sch Mol Sci, Crawley, WA 6009, Australia

[2] Wageningen Univ, Bioinformat Grp, NL-6708 PB Wageningen, Netherlands

来源：

BIOINFORMATICS ADVANCES | 2021年 / 1卷 / 01期

基金：

澳大利亚研究理事会;

关键词：

BIOSYNTHESIS; BIOLOGY; CLONING;

D O I：

10.1093/bioadv/vbab016

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

MotivationGenes 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.ResultsHere, 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.Availability and implementationcblaster source code and documentation is freely available from GitHub under the MIT license (github.com/gamcil/cblaster).Supplementary information are available at Bioinformatics Advances online.

引用

页数：10

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