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Showing 1 to 5 of 5 for “"Genome graphs"”.
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Examining bacterial variation with genome graphs and Nanopore sequencing
… found within a given species is called the pan-genome and is generally much larger than the gene repertoire of a single cell. A consequence of this pan-genome is that bacterial genomes are highly adaptable and thus variable. The dominant paradigm for analysing genetic variation relies on a …
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Genome-graph based genotyping with applications to highly variable genes in P. falciparum
Analysing genetic variation in pathogen genomes is key to understanding their biology, evolution and epidemiology. Typically, this is done by assembling one arbitrary genome, defined as the ‘reference’, and describing other samples as deviations from it. However, this model breaks down in highly …
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Co-linear Chaining on Graphs With Cycles
… in bioinformatics. As the volume of sequenced genomes grows rapidly, pairwise sequence alignment becomes inefficient for pan-genomic analyses involving multiple sequences. The graph representation of multiple genomes has been an increasingly useful tool in pan-genomics research. Therefore, …
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Function-based Algorithms for Biological Sequences
… to operate on. Due to continuous progress in genome sequencing, genome rearrangements and construction of evolutionary genome graphs, which represent the relationships between genomes, become challenging tasks. Previous approaches are largely based on distance measure so that relationship …
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A gene-space de Bruijn graph framework for improved genotyping of antimicrobial resistance genes
… greatly improved the completeness of bacterial genome assemblies, allowing for more accurate detection of AMR. However, even with long-reads, assembly remains imperfect and this can result in the under-detection of genuinely present AMR genes and inaccurate predictions of antimicrobial …