Gilchrist CLM, Booth TJ, van Wersch B, van Grieken L, Medema MH, Chooi YH. cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters.
Bioinform Adv 2021;
1:vbab016. [PMID:
36700093 PMCID:
PMC9710679 DOI:
10.1093/bioadv/vbab016]
[Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 01/28/2023]
Abstract
Motivation
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.
Results
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.
Availability and implementation
cblaster source code and documentation is freely available from GitHub under the MIT license (github.com/gamcil/cblaster).
Supplementary information
Supplementary data are available at Bioinformatics Advances online.
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