genoPlotR protocols

View genoPlotR computational protocol

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genoPlotR specifications

Information


Unique identifier OMICS_10937
Name genoPlotR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data GenoPlotR reads data stored in commonly used formats (EMBL, Genbank, BLAST and Mauve outputs) or in user-created tabular files and allows comparisons of one or several subsegments of a genome.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.8.7
Stability Stable
Requirements
methods, grid, ade4, R(≥2.10.0)
Maintained Yes

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Publication for genoPlotR

genoPlotR in pipelines

 (10)
2018
PMCID: 5765654
PMID: 29325559
DOI: 10.1186/s12915-017-0457-4

[…] for a minimum identity of 95%, e-values reported as 0 and a minimum alignment length of 2000 bp. syntenic regions shared between pairs of homologous chromosomes were visualized using the r package genoplotr []., the chromosomal locations of core, accessory and singleton genes were analyzed in the ipo323 genome for the proximity to transposable elements []. chromosomal locations were also […]

2018
PMCID: 5859366
PMID: 29593664
DOI: 10.3389/fmicb.2018.00369

[…] 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) […]

2017
PMCID: 5399880
PMID: 28439458
DOI: 10.7717/peerj.3162

[…] permutations were exported and used as input for mgr (). mgr was used to calculate the minimum number of rearrangements between the species analyzed, and to recover the rearrangement dendrogram. genoplotr () was used to plot the syntenic blocks ()., the pangenome of the nine exiguobacterium genomes from clade ii available at the time was reconstructed to aid in the taxonomic positioning […]

2017
PMCID: 5517970
PMID: 28724357
DOI: 10.1186/s12864-017-3917-x

[…] length coverage of a reference plasmid sequence were considered as potential plasmid contigs., candidate plasmid contigs were realigned with plasmid sequences with mauve 2.4.0 [] and visualized with genoplotr r package. in addition, the presence of a particular plasmid was identified by read mapping. reads from each of 28 isolates left after mapping on universal ogs were then mapped with bowtie2 […]

2017
PMCID: 5741766
PMID: 29273719
DOI: 10.1038/s41598-017-18374-y

[…] ile  in excel format., synteny was evaluated via symap and progressive mauve algorithms using current l. infantum (v.9, genedb.org) and l. major genomes as reference. synteny graphs were prepared by genoplotr, and provided as supplementary figures –., the illumina paired ends reads (fastq) and pacbio bax.h5 reads of l. infantum (jpcm5 strain) generated for this study are available at the european […]


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genoPlotR in publications

 (57)
PMCID: 5923176
PMID: 29530862
DOI: 10.1128/AAC.00209-18

[…] 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) (), […]

PMCID: 5914054
PMID: 29688842
DOI: 10.1186/s12864-018-4663-4

[…] 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 […]

PMCID: 5872301
PMID: 29600285
DOI: 10.1128/mSystems.00195-17

[…] 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 […]

PMCID: 5882170
PMID: 29565971
DOI: 10.1371/journal.pgen.1007292

[…] 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 […]

PMCID: 5859366
PMID: 29593664
DOI: 10.3389/fmicb.2018.00369

[…] 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) […]


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genoPlotR institution(s)
Department of Molecular Evolution, Uppsala University, Norbyvägen, Uppsala, Sweden
genoPlotR funding source(s)
The Swedish Research Council (623-2009-743); the Swiss National Science Foundation (PBLA33-119626); the Swedish Research Council, the Göran Gustafsson Foundation and the European Union

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