CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters
Abstract Background Co-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important examples include Biosynthetic Gene Clusters (BGCs) that produce specialized metabolites with medicinal, agricultural, and...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-05-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-023-05311-2 |
| _version_ | 1797831911596359680 |
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| author | Matthias van den Belt Cameron Gilchrist Thomas J. Booth Yit-Heng Chooi Marnix H. Medema Mohammad Alanjary |
| author_facet | Matthias van den Belt Cameron Gilchrist Thomas J. Booth Yit-Heng Chooi Marnix H. Medema Mohammad Alanjary |
| author_sort | Matthias van den Belt |
| collection | DOAJ |
| description | Abstract Background Co-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important examples include Biosynthetic Gene Clusters (BGCs) that produce specialized metabolites with medicinal, agricultural, and industrial value (e.g. antimicrobials). Comparative analysis of BGCs can aid in the discovery of novel metabolites by highlighting distribution and identifying variants in public genomes. Unfortunately, gene-cluster-level homology detection remains inaccessible, time-consuming and difficult to interpret. Results The comparative gene cluster analysis toolbox (CAGECAT) is a rapid and user-friendly platform to mitigate difficulties in comparative analysis of whole gene clusters. The software provides homology searches and downstream analyses without the need for command-line or programming expertise. By leveraging remote BLAST databases, which always provide up-to-date results, CAGECAT can yield relevant matches that aid in the comparison, taxonomic distribution, or evolution of an unknown query. The service is extensible and interoperable and implements the cblaster and clinker pipelines to perform homology search, filtering, gene neighbourhood estimation, and dynamic visualisation of resulting variant BGCs. With the visualisation module, publication-quality figures can be customized directly from a web-browser, which greatly accelerates their interpretation via informative overlays to identify conserved genes in a BGC query. Conclusion Overall, CAGECAT is an extensible software that can be interfaced via a standard web-browser for whole region homology searches and comparison on continually updated genomes from NCBI. The public web server and installable docker image are open source and freely available without registration at: https://cagecat.bioinformatics.nl . |
| first_indexed | 2024-04-09T13:59:20Z |
| format | Article |
| id | doaj.art-ce3ee01c945f4592902421521f44c479 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-09T13:59:20Z |
| publishDate | 2023-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-ce3ee01c945f4592902421521f44c4792023-05-07T11:25:48ZengBMCBMC Bioinformatics1471-21052023-05-012411810.1186/s12859-023-05311-2CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clustersMatthias van den Belt0Cameron Gilchrist1Thomas J. Booth2Yit-Heng Chooi3Marnix H. Medema4Mohammad Alanjary5Bioinformatics Group, Wageningen University and ResearchSchool of Molecular Sciences, The University of Western AustraliaSchool of Molecular Sciences, The University of Western AustraliaSchool of Molecular Sciences, The University of Western AustraliaBioinformatics Group, Wageningen University and ResearchBioinformatics Group, Wageningen University and ResearchAbstract Background Co-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important examples include Biosynthetic Gene Clusters (BGCs) that produce specialized metabolites with medicinal, agricultural, and industrial value (e.g. antimicrobials). Comparative analysis of BGCs can aid in the discovery of novel metabolites by highlighting distribution and identifying variants in public genomes. Unfortunately, gene-cluster-level homology detection remains inaccessible, time-consuming and difficult to interpret. Results The comparative gene cluster analysis toolbox (CAGECAT) is a rapid and user-friendly platform to mitigate difficulties in comparative analysis of whole gene clusters. The software provides homology searches and downstream analyses without the need for command-line or programming expertise. By leveraging remote BLAST databases, which always provide up-to-date results, CAGECAT can yield relevant matches that aid in the comparison, taxonomic distribution, or evolution of an unknown query. The service is extensible and interoperable and implements the cblaster and clinker pipelines to perform homology search, filtering, gene neighbourhood estimation, and dynamic visualisation of resulting variant BGCs. With the visualisation module, publication-quality figures can be customized directly from a web-browser, which greatly accelerates their interpretation via informative overlays to identify conserved genes in a BGC query. Conclusion Overall, CAGECAT is an extensible software that can be interfaced via a standard web-browser for whole region homology searches and comparison on continually updated genomes from NCBI. The public web server and installable docker image are open source and freely available without registration at: https://cagecat.bioinformatics.nl .https://doi.org/10.1186/s12859-023-05311-2Gene clusterSecondary metaboliteHomology searchColocalizedBiosyntheticComparative analysis |
| spellingShingle | Matthias van den Belt Cameron Gilchrist Thomas J. Booth Yit-Heng Chooi Marnix H. Medema Mohammad Alanjary CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters BMC Bioinformatics Gene cluster Secondary metabolite Homology search Colocalized Biosynthetic Comparative analysis |
| title | CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters |
| title_full | CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters |
| title_fullStr | CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters |
| title_full_unstemmed | CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters |
| title_short | CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters |
| title_sort | cagecat the comparative gene cluster analysis toolbox for rapid search and visualisation of homologous gene clusters |
| topic | Gene cluster Secondary metabolite Homology search Colocalized Biosynthetic Comparative analysis |
| url | https://doi.org/10.1186/s12859-023-05311-2 |
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