genoPlotR

[…] were included., phylograms were visualized using evolview (http://www.evolgenius.info), and histograms and gene synteny were visualized using the statistical software r (v3.3.3; packages ggplot2 and genoplotr) (r foundation for statistical computing, vienna, austria). the location of the ars operon on the e. coli chromosome was visualized using the blast ring image generator (brig) (v0.95) (), […]

[…] based on specified parameters, such as minimum block size and gap threshold (a maximum distance between genes in a synteny block). synteny blocks obtained by grimm-synteny were visualized using genoplotr []. the multiple genome rearrangement (mgr) program [] was used to determine the number and types of rearrangements that caused the synteny block reshuffling among three species. to run […]

[…] contigs of interest using rast (). regions of similarity between host and clone dna were identified using mauve (). data analyses were performed in r, including packages rsamtools, gviz, ape, and genoplotr., raw sequence data have been deposited at the ncbi sequence read archive under accession numbers srx3141910 (clgm3 clone 2) and srx3141914 (clgm3 clone 5). sequence data and other data may […]

[…] the t-coffee multiple sequence aligner []. protein secondary structures were predicted using jpred(v4) []. synteny comparisons were performed using the artemis comparison tool [] and plotted with genoplotr []. β-galactosidase assays were performed as previously described with three to six biological replicates per treatment [, ]. mesorhizobium conjugation experiments were performed […]

[…] gene synteny analysis was assessed with progressivemauve (http://darlinglab.org/mauve/), (darling et al., ). to compare and visualize genomic regions from mauve results we used the r-package genoplotr (http://genoplotr.r-forge.r-project.org/) (guy et al., )., the genome sequence similarity between amycolatopsis strains was evaluated with the genome-to-genome distance calculator (ggdc) […]

[…] along with annotation of the conserved l1 and l2 signatures (constant et al., ) were done in arb (ludwig et al., ). the gene synteny of the structural and maturation genes was visualized with the genoplotr package in r (guy et al., ). locus tag for the genes identified across the acidobacterial genomes encoding for group 1h/5 [nife]‐hydrogenases can be found in supporting information table […]