clinker & clustermap.js: automatic generation of gene cluster comparison figures
Abstract Summary Genes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their function and evolutionary history. However, comparison and visualization of gene cluster similarity is a tedious process, particularly when ma...
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| Published in | Bioinformatics (Oxford, England) Vol. 37; no. 16; pp. 2473 - 2475 |
|---|---|
| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
25.08.2021
Oxford Publishing Limited (England) |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Abstract
Summary
Genes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their function and evolutionary history. However, comparison and visualization of gene cluster similarity is a tedious process, particularly when many clusters are being compared. Here, we present clinker, a Python based tool and clustermap.js, a companion JavaScript visualization library, which used together can automatically generate accurate, interactive, publication-quality gene cluster comparison figures directly from sequence files.
Availability and implementation
Source code and documentation for clinker and clustermap.js is available on GitHub (github.com/gamcil/clinker and github.com/gamcil/clustermap.js, respectively) under the MIT license. clinker can be installed directly from the Python Package Index via pip.
Supplementary information
Supplementary data are available at Bioinformatics online. |
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| AbstractList | Abstract
Summary
Genes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their function and evolutionary history. However, comparison and visualization of gene cluster similarity is a tedious process, particularly when many clusters are being compared. Here, we present clinker, a Python based tool and clustermap.js, a companion JavaScript visualization library, which used together can automatically generate accurate, interactive, publication-quality gene cluster comparison figures directly from sequence files.
Availability and implementation
Source code and documentation for clinker and clustermap.js is available on GitHub (github.com/gamcil/clinker and github.com/gamcil/clustermap.js, respectively) under the MIT license. clinker can be installed directly from the Python Package Index via pip.
Supplementary information
Supplementary data are available at Bioinformatics online. Genes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their function and evolutionary history. However, comparison and visualization of gene cluster similarity is a tedious process, particularly when many clusters are being compared. Here, we present clinker, a Python based tool and clustermap.js, a companion JavaScript visualization library, which used together can automatically generate accurate, interactive, publication-quality gene cluster comparison figures directly from sequence files.SUMMARYGenes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their function and evolutionary history. However, comparison and visualization of gene cluster similarity is a tedious process, particularly when many clusters are being compared. Here, we present clinker, a Python based tool and clustermap.js, a companion JavaScript visualization library, which used together can automatically generate accurate, interactive, publication-quality gene cluster comparison figures directly from sequence files.Source code and documentation for clinker and clustermap.js is available on GitHub (github.com/gamcil/clinker and github.com/gamcil/clustermap.js, respectively) under the MIT license. clinker can be installed directly from the Python Package Index via pip.AVAILABILITY AND IMPLEMENTATIONSource code and documentation for clinker and clustermap.js is available on GitHub (github.com/gamcil/clinker and github.com/gamcil/clustermap.js, respectively) under the MIT license. clinker can be installed directly from the Python Package Index via pip.Supplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. Genes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their function and evolutionary history. However, comparison and visualization of gene cluster similarity is a tedious process, particularly when many clusters are being compared. Here, we present clinker, a Python based tool and clustermap.js, a companion JavaScript visualization library, which used together can automatically generate accurate, interactive, publication-quality gene cluster comparison figures directly from sequence files. Source code and documentation for clinker and clustermap.js is available on GitHub (github.com/gamcil/clinker and github.com/gamcil/clustermap.js, respectively) under the MIT license. clinker can be installed directly from the Python Package Index via pip. Supplementary data are available at Bioinformatics online. Genes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their function and evolutionary history. However, comparison and visualization of gene cluster similarity is a tedious process, particularly when many clusters are being compared. Here, we present clinker, a Python based tool and clustermap.js, a companion JavaScript visualization library, which used together can automatically generate accurate, interactive, publication-quality gene cluster comparison figures directly from sequence files. Availability and implementation Source code and documentation for clinker and clustermap.js is available on GitHub (github.com/gamcil/clinker and github.com/gamcil/clustermap.js, respectively) under the MIT license. clinker can be installed directly from the Python Package Index via pip. Supplementary information Supplementary data are available at Bioinformatics online. |
| Author | Chooi, Yit-Heng Gilchrist, Cameron L M |
| Author_xml | – sequence: 1 givenname: Cameron L M orcidid: 0000-0001-7798-427X surname: Gilchrist fullname: Gilchrist, Cameron L M email: cameron.gilchrist@research.uwa.edu.au – sequence: 2 givenname: Yit-Heng orcidid: 0000-0001-7719-7524 surname: Chooi fullname: Chooi, Yit-Heng email: yitheng.chooi@uwa.edu.au |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33459763$$D View this record in MEDLINE/PubMed |
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| References | Gilchrist (2023051609061249400_btab007-B9) 2018; 16 Ziemert (2023051609061249400_btab007-B20) 2016; 33 Kautsar (2023051609061249400_btab007-B13) 2019; 48 Carver (2023051609061249400_btab007-B4) 2005; 21 Li (2023051609061249400_btab007-B14) 2019; 21 Garcia (2023051609061249400_btab007-B8) 2019; 35 Bostock (2023051609061249400_btab007-B2) 2011; 17 Sullivan (2023051609061249400_btab007-B18) 2011; 27 Cock (2023051609061249400_btab007-B5) 2009; 25 Camacho (2023051609061249400_btab007-B3) 2009; 10 Doroghazi (2023051609061249400_btab007-B7) 2013; 14 Harrison (2023051609061249400_btab007-B12) 2018; 34 Guy (2023051609061249400_btab007-B11) 2010; 26 Gilchrist (2023051609061249400_btab007-B10) 2020 de Vries (2023051609061249400_btab007-B6) 2017; 18 Blin (2023051609061249400_btab007-B1) 2019; 47 Virtanen (2023051609061249400_btab007-B19) 2020; 17 Nielsen (2023051609061249400_btab007-B16) 2017; 2 Medema (2023051609061249400_btab007-B15) 2013; 30 Pritchard (2023051609061249400_btab007-B17) 2006; 22 |
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Genes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their... Genes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their function and... |
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