DNAPlotter protocols

View DNAPlotter computational protocol

DNAPlotter statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Circular genome visualization chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

DNAPlotter specifications

Information


Unique identifier OMICS_00906
Name DNAPlotter
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format EMBL, Genbank, GFF
Output data Images
Output format JPEG, PNG, BMP, WBMP, PostScript
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Tim Carver <>

Publication for DNAPlotter

DNAPlotter in pipelines

 (18)
2018
PMCID: 5865083
PMID: 29576807
DOI: 10.7150/jgen.24935

[…] means of the hierarchical genome assembly process . the genome was annotated by using the rast server or ncbi's prokaryotic genome annotation pipeline (pgap) . a chromosome map was drawn by using dnaplotter . secondary metabolites were predicted by using antismash . clustered regularly interspaced short palindromic repeat (crispr) loci were detected by using crisprfinder . functional […]

2017
PMCID: 5495459
PMID: 28671965
DOI: 10.1371/journal.pone.0180493

[…] parameters., for a. thereius lmg 24486t, clustered regularly insterspaced short palindromic repeat (crispr) regions were identified through crisprfinder [] and a genome plot was generated with dnaplotter []. the origin of chromosomal replication was predicted with the ori-finder tool []. genomic islands were searched for with islandviewer [] and bacteriocins with bagel3 []., a maximum […]

2016
PMCID: 4910999
PMID: 27309375
DOI: 10.1371/journal.pone.0157600

[…] the normalised coverage after dividing the per position coverage by the total mapped reads of each.bam file. we visualised the coverage plots in comparison to gc content across the genome using dnaplotter v10.2 []., we would like to thank professor patricia cane, dr. chris parry, andros gavriel, adriana alvarez and other members of the antiviral unit in the virus reference department, phe […]

2016
PMCID: 4932437
PMID: 27419068
DOI: 10.1016/j.gdata.2016.06.002

[…] 2 of 173 kpb aligned with its plasmid (pbpsh), suggesting that contig 2 might be a plasmid itself. gc content along the genome averaged 37.16%. circular visualizations of the genome generated by dnaplotter can be observed in ., we can observe in that after annotation l. sphaericus iii(3)7 has 4485 coding sequences, 149 rna coding genes and 87 pseudogenes. contains the cog functional […]

2016
PMCID: 4943601
PMID: 27409077
DOI: 10.1371/journal.pone.0158866

[…] neighbor pasteurella pneumotropica (pp), aa and escherichia coli (ec) was performed using reciprocal smallest distance []. the predicted features were visualized in a genomic context using dnaplotter []. the domain structures of the orfs were predicted by pfam. synteny scores were calculated by quota synteny alignment []. the bacteriophage regions were identified by phast []. […]


To access a full list of citations, you will need to upgrade to our premium service.

DNAPlotter in publications

 (107)
PMCID: 5893538
PMID: 29636463
DOI: 10.1038/s41426-018-0065-6

[…] and plasmid-encoded replication initiation protein. the ori and the dnaa box sequences were predicted using ori-finder, and at-rich repetitive sequences were identified using tandem repeats finder,. dnaplotter was used to visualise the plasmid genome., to examine whether the plasmid identified in c. concisus strains p2cdo4, p20cdo-s2 and p20cdo-s3 shared similarities with known plasmids, […]

PMCID: 5881045
PMID: 29500254
DOI: 10.1128/AEM.02655-17

[…] number kx013538), peg430-1 (genbank accession number lt174530), and ppgrt46 (genbank accession number km023153) were used as the reference plasmids for annotation. plasmid maps were prepared using dnaplotter and circos. the tn number was designated by the transposon registry ()., the ability of mcr-1 to undergo horizontal gene transfer was assessed by broth and filter mating using a standard […]

PMCID: 5865083
PMID: 29576807
DOI: 10.7150/jgen.24935

[…] means of the hierarchical genome assembly process . the genome was annotated by using the rast server or ncbi's prokaryotic genome annotation pipeline (pgap) . a chromosome map was drawn by using dnaplotter . secondary metabolites were predicted by using antismash . clustered regularly interspaced short palindromic repeat (crispr) loci were detected by using crisprfinder . functional […]

PMCID: 5918139
PMID: 29707211
DOI: 10.1016/j.nmni.2018.02.007

[…] for an alignment length >80 amino acids. if alignment lengths were <80 aa, we used an e value of 1e-05. such parameter thresholds have been used in previous work to define orfans. artemis and dnaplotter were used for data management and visualization of genomic features, respectively., a phylogenomic tree was constructed using an fasttree based on mauve programme genome alignment ., […]

PMCID: 5874624
PMID: 29361673
DOI: 10.3390/microorganisms6010010

[…] on previous pfge and mapping experiments in other n. gonorrhoeae strains [,]. the predicted fragment sizes and their locations in the genome sequence [] were noted and mapped to the chromosome using dnaplotter [] ()., cultures were grown for eight weeks under standard conditions and for eight weeks with sub-lethal 128 μg/ml nalidixic acid. dna extraction used the gentra puregene yeast/bact. kit […]


To access a full list of publications, you will need to upgrade to our premium service.

DNAPlotter institution(s)
Wellcome Trust Sanger Institute, UK; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
DNAPlotter funding source(s)
The Wellcome trust

DNAPlotter reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review DNAPlotter