GenDiMug: a generic inclusive multigraph framework to analyze genomic organizations and -omics data at multiple scales
After decades of investigation, analyses of genome organization remain challenging. This is because genome descriptions are very information-rich and usually rendered as a linear map of genomic features corresponding to an ordered list of position intervals on a nucleic acid macromolecular backbone. This formalism, while accurate, is not fully optimized to mathematically analyze all genome…
GenDiMug, a new framework for analyzing genomic and -omics data, addresses the challenges in genome organization research. This innovative tool employs a network representation of the genome as its backbone, offering a versatile platform to integrate spatial and ontogenetic relationships between genomic features and multi-omics data.
By utilizing GenDiMug, researchers can visualize genomic topology at both contig and chromosomal scales, with remarkable precision at the base-pair level. The framework also enables the analysis of genome positional effects through various graph metrics. In a demonstration of the tool's capabilities, GenDiMug revealed clustering of genes with comparable expression levels in eukaryotic genomes and their potential circadian regulation in a photosynthetic alga.
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