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Protocols

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

Versioning


No version available

Documentation


Publication for genoPlotR

genoPlotR citations

 (76)
library_books

Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain

2018
Antimicrob Agents Chemother
PMCID: 5923176
PMID: 29530862
DOI: 10.1128/AAC.00209-18

[…] e) 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) (), wi […]

call_split

Partial arm translocations in evolution of malaria mosquitoes revealed by high coverage physical mapping of the Anopheles atroparvus genome

2018
BMC Genomics
PMCID: 5914054
PMID: 29688842
DOI: 10.1186/s12864-018-4663-4
call_split See protocol

[…] locks 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 the […]

call_split

Developing a Bacteroides System for Function Based Screening of DNA from the Human Gut Microbiome

2018
mSystems
PMCID: 5872301
PMID: 29600285
DOI: 10.1128/mSystems.00195-17
call_split See protocol

[…] for 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. […]

library_books

Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements

2018
PLoS Genet
PMCID: 5882170
PMID: 29565971
DOI: 10.1371/journal.pgen.1007292

[…] ing 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 as previous […]

library_books

Comparative Genomics and Biosynthetic Potential Analysis of Two Lichen Isolated Amycolatopsis Strains

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

[…] analysis.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) 2.1 o […]

library_books

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

2018
Environ Microbiol
PMCID: 5900883
PMID: 29327410
DOI: 10.1111/1462-2920.14043

[…] its 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 S9. […]

Citations

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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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