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 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.

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

“…As a result, we found homologues spanning up to six genes in Aspergillus ustus, Aspergillus calidoustus, Aspergillus insuetus and Aspergillus pseudodeflectus, all of which are members of section Usti as well as known producers of acyl drimane sesquiterpenoids. Further analyses of these clusters using clinker (Gilchrist and Chooi 2021) gave us confidence that our candidate BGC did indeed encode the biosynthesis of the nanangenines.…”

“…In this manner, cblaster can uncover deep-seated evolutionary relationships that may not be immediately apparent, such as proteins or sub-clusters that have been co-opted between different pathways. Furthermore, cblaster can generate comparative gene cluster visualisations using clinker (Gilchrist and Chooi 2021). These visualisations show the detected clusters in their genomic context, enabling a fuller view of the overall conservation of cluster architecture across taxa.…”

“…Overview of modules provided by the cblaster command-line interface.Module Description searchThe main cblaster search workflow makedb Create local search databases from personal sequence data gne Gene neighbourhood estimation of cblaster search results extract Extract sequences from cblaster search results gui Launcher for the cblaster graphical user interface (GUI) extract clusters Extract detected gene clusters from cblaster sessions plot clusters Plot detected gene clusters using clinker(Gilchrist and Chooi 2021) …”

An inventory of early branch points in microbial phosphonate biosynthesis

“…In summary, these results help contextualize current knowledge of early branch points of phosphonate biosynthesis and provide a framework to generate hypotheses and triage discovery efforts. shown aligned (with arbitrary color scheme) using clinker [50] to highlight the conserved seven-gene core, which is expanded below to show annotations and putative phosphonate product. The accession numbers WP_004525540 and WP_004523200 represent the most common Ppm in AEPT-and PhnY-containing clusters, respectively.…”

Discovery and Biosynthesis of a Structurally Dynamic Antibacterial Diterpenoid

“…In order to evaluate whether the eight highly homologous TSs of Bnd4 are predicted to biosynthesize 1,w ef irst annotated their genetic neighborhoods and aligned the BGCs with Clinker (Figure 5). [28] In fact, each of the BGCs encodes the core biosynthetic genes with each of the BGCs from Streptomyces identical in genetic organization, with the exception of the lack of the transporter in Streptomyces sp. CNH287 and Streptomyces sp.yr375.…”