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PseudoViewer specifications

Information


Unique identifier OMICS_04462
Name PseudoViewer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Kyungsook Han <>

Information


Unique identifier OMICS_04462
Name PseudoViewer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Kyungsook Han <>

Publications for PseudoViewer

PseudoViewer in publications

 (17)
PMCID: 5641321
PMID: 29067018
DOI: 10.3389/fmicb.2017.01960

[…] (ncbi) orf finder program. motif searches were performed in three databases, including prosite, pfam and cdd. rna pseudoknot structure was predicted using the dotknot program and drawn with pseudoviewer3 (; )., phylogenetic trees were constructed based on the deduced amino acid sequences of the putative rdrp and cp regions using the maximum-likelihood (ml) method of the mega program […]

PMCID: 5561095
PMID: 28819307
DOI: 10.1038/s41598-017-09268-0

[…] and settings: 37 °c temperature; kuhn length 6; jacobson-stockmayer gamma = 1.75 and contiguous stems = 6. visualization of the secondary structures with pseudoknots was performed using the pseudoviewer software (inha university, s korea http://wilab.inha.ac.kr/pseudoviewer/). the rnacomposer (poland, http://rnacomposer.cs.put.poznan.pl/) was used to generate the pbd-files […]

PMCID: 5450055
PMID: 28558664
DOI: 10.1186/s12859-017-1682-0

[…] rna visualization tools that have been developed, and two excellent reviews of them can be found in [, ], with notable examples that are still available including varna [], jviz.rna [–], forna [], pseudoviewer [–], 4sale [, ], assemble2 [, ], rna2dmap [], r2r [], and r-chie []. all visualization software developed for rna have as their goal to display an informative structure of the rna […]

PMCID: 5404819
PMID: 28441395
DOI: 10.1371/journal.pone.0175662

[…] the its2 secondary structures can be used for phylogenetic purposes together with the sequence itself. rna secondary structure predictions were performed using mfold software [] and visualised in pseudoviewer 3 web application (http://pseudoviewer.inha.ac.kr/)., based on secondary structure reconstructions, the its2 region of all the sequences available were manually aligned in bioedit […]

PMCID: 5215925
PMID: 28056060
DOI: 10.1371/journal.pone.0169042

[…] used as its2 secondary structure analysis for group 1, group 2 and group3 were eu498090.1, eu021461.1, and fj379263.1, respectively. putative secondary structures were finally visualized using pseudoviewer 3 [] and adobe illustrator® v. 16.0.1., to analyze the phylogenetic relationships of ganoderma lucidum species, a total of 241 its1 sequences, including 234 downloaded from ncbi database […]


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PseudoViewer institution(s)
Department of Computer Science and Engineering, Inha University, Inchon, Korea; Department of Automation Engineering, Inha University, Inchon, Korea

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