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

Cameron L.M. Gilchrist; Thomas J. Booth; Bram van Wersch; Liana van Grieken; Marnix H. Medema; Yit-Heng Chooi

doi:10.1093/bioadv/vbab016

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

Cameron L.M. Gilchrist^*, Thomas J. Booth, Bram van Wersch, Liana van Grieken, Marnix H. Medema^*, Yit-Heng Chooi^*

^*Corresponding author for this work

Bioinformatics

Research output: Contribution to journal › Article › Academic › peer-review

89 Citations (Scopus)

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).

Original language	English
Article number	vbab016
Journal	Bioinformatics Advances
Volume	1
Issue number	1
DOIs	https://doi.org/10.1093/bioadv/vbab016
Publication status	Published - 9 Jun 2021

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Access to Document

10.1093/bioadv/vbab016Licence: CC BY

https://edepot.wur.nl/569714Licence: CC BY

Cite this

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abstract = "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).",

author = "Gilchrist, {Cameron L.M.} and Booth, {Thomas J.} and {van Wersch}, Bram and {van Grieken}, Liana and Medema, {Marnix H.} and Yit-Heng Chooi",

year = "2021",

month = jun,

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doi = "10.1093/bioadv/vbab016",

language = "English",

volume = "1",

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T1 - cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters

AU - Gilchrist, Cameron L.M.

AU - Booth, Thomas J.

AU - van Wersch, Bram

AU - van Grieken, Liana

AU - Medema, Marnix H.

AU - Chooi, Yit-Heng

PY - 2021/6/9

Y1 - 2021/6/9

N2 - 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).

AB - 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).

U2 - 10.1093/bioadv/vbab016

DO - 10.1093/bioadv/vbab016

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

Abstract

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