The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
clinker & clustermap.js: automatic generation of gene cluster comparison figures
Open accessAbstract
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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SciPy 1.0: fundamental algorithms for scientific computing in Python
Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., et al. (2020) · Nature Methods · doi:10.1038/s41592-019-0686-2 · Cited by 38,430
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
Biopython: freely available python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080
Cited by
Gaborieau, B., Vaysset, H., Tesson, F., Charachon, I., Dib, N., Bernier, J., Dequidt, T., Georjon, H., Clermont, O., Hersen, P., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01832-5 · Cited by 141
Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery
Hatano, T., Palani, S., Papatziamou, D., Salzer, R., Souza, D. P., Tamarit, D., Makwana, M., Potter, A., Haig, A., Xu, W., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30656-2 · Cited by 104
Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome
Laso-Pérez, R., Wu, F., Crémière, A., Speth, D. R., Magyar, J. S., Zhao, K., Krupovic, M., & Orphan, V. J. (2023) · Nature Microbiology · doi:10.1038/s41564-022-01297-4 · Cited by 68
The confluence of big data and evolutionary genome mining for the discovery of natural products
Chevrette, M. G., Gavrilidou, A., Mantri, S., Selem-Mojica, N., Ziemert, N., & Barona-Gómez, F. (2021) · Natural Product Reports · doi:10.1039/d1np00013f · Cited by 66
Metadata
- Authors
- Gilchrist, C. L. M., & Chooi, Y.-H.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-01-18
- Volume
- 37
- Issue
- 16
- Pages
- 2473-2475
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W3121652846
- Cited by
- 1,600
- References
- 3
- FWCI
- 53.13
- Type
- journal article
- Language
- en
- Open access
- bronze
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