GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective

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Abstract

Synteny conservation analysis is a well-established methodology to investigate the potential functional role of unknown prokaryotic genes. However, bioinformatic tools to reconstruct and visualise genomic contexts usually depend on slow computations, are restricted to narrow taxonomic ranges, and/or do not allow for the functional and interactive exploration of neighbouring genes across different species. Here, we present GeCoViz, an online resource built upon 12 221 reference prokaryotic genomes that provides fast and interactive visualisation of custom genomic regions anchored by any target gene, which can be sought by either name, orthologous group (KEGGs, eggNOGs), protein domain (PFAM) or sequence. To facilitate functional and evolutionary interpretation, GeCoViz allows to customise the taxonomic scope of each analysis and provides comprehensive annotations of the neighbouring genes. Interactive visualisation options include, among others, the scaled representations of gene lengths and genomic distances, and on the fly calculation of synteny conservation of neighbouring genes, which can be highlighted based on custom thresholds. The resulting plots can be downloaded as high-quality images for publishing purposes. Overall, GeCoViz offers an easy-to-use, comprehensive, fast and interactive web-based tool for investigating the genomic context of prokaryotic genes, and is freely available at https://gecoviz.cgmlab.org

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APA

Botas, J., Rodríguez Del Río, Á., Giner-Lamia, J., & Huerta-Cepas, J. (2022). GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective. Nucleic Acids Research, 50(W1), W352–W357. https://doi.org/10.1093/nar/gkac367

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