Genome Complexity Browser: Visualization and quantification of genome variability
Comparative genomics studies may be used to acquire new knowledge regarding genome architecture, which defines the rules for combining sets of genes in the genome of living organisms. Hundreds of thousands of prokaryotic genomes have been sequenced and assembled. However, computational tools capable...
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| Veröffentlicht in: | PLoS computational biology 2020-10, Vol.16 (10), p.e1008222-e1008222 |
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| creator | Manolov, Alexander Konanov, Dmitry Fedorov, Dmitry Osmolovsky, Ivan Vereshchagin, Rinat Ilina, Elena |
| description | Comparative genomics studies may be used to acquire new knowledge regarding genome architecture, which defines the rules for combining sets of genes in the genome of living organisms. Hundreds of thousands of prokaryotic genomes have been sequenced and assembled. However, computational tools capable of simultaneously comparing large numbers of genomes are lacking. We developed the Genome Complexity Browser, a tool that allows the visualization of gene contexts, in a graph-based format, and the quantification of variability for different segments of a genome. The graph-based visualization allows the inspection of changes in gene contents and neighborhoods across hundreds of genomes, simultaneously, which may facilitate the identification of conserved and variable segments of operons or the estimation of the overall variability associated with a particular genome locus. We introduced a measure called complexity, to quantify genome variability. Intraspecies and interspecies comparisons revealed that regions with high complexity values tended to be located in areas that are conserved across different strains and species. |
| doi_str_mv | 10.1371/journal.pcbi.1008222 |
| format | Article |
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| subjects | Algorithms Biology and Life Sciences Cell division Chromosomes Complexity Computer and Information Sciences Computer applications Databases, Genetic Gene expression Genetic variation Genetic Variation - genetics Genome, Bacterial - genetics Genomes Genomics Genomics - methods Inspection Medicine Methods Operons Physical Sciences Research and Analysis Methods Segments Software Technology application User-Computer Interface Variability Visualization |
| title | Genome Complexity Browser: Visualization and quantification of genome variability |
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