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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

Versioning


No version available

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 citations

 (23)
library_books

Molecular Characterization of Novel Totivirus Like Double Stranded RNAs from Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust

2017
Front Microbiol
PMCID: 5641321
PMID: 29067018
DOI: 10.3389/fmicb.2017.01960

[…] formation (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 (; ). […]

library_books

CRISPR/Cas9 editing reveals novel mechanisms of clustered microRNA regulation and function

2017
Sci Rep
PMCID: 5561095
PMID: 28819307
DOI: 10.1038/s41598-017-09268-0

[…] vsfold5/) 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 through molecu […]

library_books

Numerical integration methods and layout improvements in the context of dynamic RNA visualization

2017
BMC Bioinformatics
PMCID: 5450055
PMID: 28558664
DOI: 10.1186/s12859-017-1682-0

[…] ny 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 molecul […]

library_books

Molecular phylogeny of Oncaeidae (Copepoda) using nuclear ribosomal internal transcribed spacer (ITS rDNA)

2017
PLoS One
PMCID: 5404819
PMID: 28441395
DOI: 10.1371/journal.pone.0175662

[…] use 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/). […]

library_books

Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single Nucleotide Polymorphism in Ganoderma lucidum

2017
PLoS One
PMCID: 5215925
PMID: 28056060
DOI: 10.1371/journal.pone.0169042

[…] uences 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. […]

library_books

Chloroplast genome expansion by intron multiplication in the basal psychrophilic euglenoid Eutreptiella pomquetensis

2017
PeerJ
PMCID: 5572947
PMID: 28852596
DOI: 10.7717/peerj.3725

[…] served 5′ insertion sequence GUGYG. RNA secondary structure for group II introns was created by RNA folding via Mfold web server using default settings (), manually optimized and illustrated with the PseudoViewer web application (). For roaA a pairwise sequence comparison of the amino acid sequence of E. gracilis with a putative amino acid sequence of Etl. pomquetensis was performed using Exonerat […]

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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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