OGDRAW protocols

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OGDRAW specifications

Information


Unique identifier OMICS_06235
Name OGDRAW
Alternative name OrganellarGenomeDraw
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Medium
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_06235
Name OGDRAW
Alternative name OrganellarGenomeDraw
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Publication for OrganellarGenomeDraw

OGDRAW in pipelines

 (30)
2018
PMCID: 5854438
PMID: 29543905
DOI: 10.1371/journal.pone.0194613

[…] were assembled after being aligned to the reference genome using geneious 4.8 [] and annotated using the dual organellar genome annotator (dogma) database []. the cp genome map was generated using ogdraw (http://ogdraw.mpimp-golm.mpg.de/) []. the raw sequencing data were deposited in genbank sra database (samn08348372–samn08348378, https://submit.ncbi.nlm.nih.gov/subs/sra). the annotated seven […]

2018
PMCID: 5889905
PMID: 29770326
DOI: 10.1155/2018/1507847

[…] with homologous genes from other sequenced chloroplast genomes. the annotation of the trna genes was verified using trnascan-se []. the circular cp genome map was constructed by the use of online ogdraw program []. finally, the annotated genome sequences were submitted to the ncbi genbank under accession number mf596485., the genome features such as gc contents and size of s. teitensis cp […]

2017
PMCID: 5345388
PMID: 28286710
DOI: 10.7717/peerj.3037

[…] (). the trnas and their corresponding structures were further verified and predicted using the trnascan-se 1.21 program (). the physical maps were drawn using the web tool organellar genome draw (ogdraw) v1.2 ()., ssrs in m. cathayana and m. multicaulis cp genomes were detected using misa () with the minimal repeat number set to 10, 5, 4, 3, 3, and 3 for mono-, di-, tri-, tetra-, penta-, […]

2017
PMCID: 5347249
PMID: 28280029
DOI: 10.1128/genomeA.01745-16

[…] chloroplast genome. chloroplast gene annotation was primarily achieved with dogma (). additionally, trnascan-se () was used for trna gene annotation. the chloroplast gene map was drawn using ogdraw ()., the p. crassum chloroplast genome is 79,397 bp in length. the genome adenine-thymine (at) content (74.1%) is rather high among green algae, whereas the amount of intergenic sequence (16%) […]

2017
PMCID: 5374973
PMID: 28367378
DOI: 10.7717/peerj.3148

[…] checked by mitofy firstly from other mt genomes sequenced. all transfer rna genes were confirmed by using trnascan-se with default settings (). the circular mt genome map was drawn through the ogdraw online program ().the final mt genome of s. suchowensis has been deposited to genbank (accession number: nc_029317.1), simple sequence repeats (ssrs) of the s. suchowensis mt genome […]


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OGDRAW in publications

 (151)
PMCID: 5943242
PMID: 29743507
DOI: 10.1038/s41598-018-25585-4

[…] information from the close relative a. thaliana. the complete structure of trna genes was validated using trnascan-se v1.2.1. the systematic circular view of the chloroplast genome was created using ogdraw and in-house customized perl script. comparative syntenic maps were generated using circos following the blastz annotation. a chloroplast-based browser was developed for systematic analysis […]

PMCID: 5940233
PMID: 29738547
DOI: 10.1371/journal.pone.0196995

[…] and rfam cmscan v1.1 []. several important genes and ambiguous sequences were re-confirmed with pcr amplification followed by sanger sequencing. the annotated plastid genomes were visualized using organellargenomedraw v1.2 []. comparative analysis of the genome structure was accomplished using unimog v1.0 [] and mauve genome alignment v2.2.0 [, ] through the geneious plug-in using the default […]

PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] for trnas; the geneious annotation tool was used to determine the plastomes of c. triplicata and oncidium gower ramsey (genbank id: nc_014056.1) as references. linear plastome maps were drawn using ogdraw., mitochondria were isolated from all g. elata tissues except the rhizome using previously described centrifugation methods. a modified ctab method was used to extract mt-dnas. the purified […]

PMCID: 5885378
PMID: 29618324
DOI: 10.1186/s12864-018-4633-x

[…] cp genome using geneious v9.0.5 software (biomatters, auckland, new zealand). the trna genes were verified with trnascan-se v1.21 [] with default settings. the circular gene maps were drawn by the organellargenomedraw tool (ogdraw) following by manual modification []., multiple complete chloroplast genomes of saxifragaceae provide an opportunity to compare the sequence variation within […]

PMCID: 5875761
PMID: 29596414
DOI: 10.1371/journal.pone.0192966

[…] p. taeda and p. contorta. transfer rna sequences of the p. taeda cp genome were verified using trnascan-se version 1.21 [] with default settings, and the structural features were illustrated using ogdraw []. to examine deviations in synonymous codon usage by avoiding the influence of amino acid composition, the relative synonymous codon usage was determined using mega 6 software [], […]


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OGDRAW institution(s)
Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany

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