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RNAView specifications

Information


Unique identifier OMICS_05576
Name RNAView
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline RView Team

Publication for RNAView

RNAView citations

 (16)
call_split

CompAnnotate: a comparative approach to annotate base pairing interactions in RNA 3D structures

2017
Nucleic Acids Res
PMCID: 5737500
PMID: 28641399
DOI: 10.1093/nar/gkx538
call_split See protocol

[…] rovements for sequence alignment are shown in ). With the support of input alignment, CompAnnotate does further aligning of base pairs considering the annotations from the existing tool (MC-Annotate, RNAView, FR3D, DSSR or ClaRNA). For each base pair of one RNA, a compatible base pair in the other RNA is searched, using the base correspondence as a guide. The resulting fine-tuned alignment of base […]

library_books

Modelling the three dimensional structure of the right terminal domain of pospiviroids

2017
Sci Rep
PMCID: 5429643
PMID: 28386073
DOI: 10.1038/s41598-017-00764-x

[…] ce for bulges; usage of updated (2012) force field; 1,000 structures; 10,000 MC cycles. From the predicted 3D structure(s), we extracted information on types of base pairs and further interactions by rnaview and x3dna-dssr.RNAredesign samples the possible sequence space that stabilizes a given 3D structure with a fixed structure backbone. […]

call_split

Using sequence signatures and kink turn motifs in knowledge based statistical potentials for RNA structure prediction

2017
Nucleic Acids Res
PMCID: 5435971
PMID: 28158755
DOI: 10.1093/nar/gkx045
call_split See protocol

[…] The initial tree graph is generated based on the 2D structure information given in BPSEQ format. To generate 2D structures, we use available tools such as RNAView (), FR3D () and MC-Annotate () based on known 3D structures. We also tested our approach by predicting 2D structures by RNAfold () based on the dynamic programming algorithm proposed by Nussin […]

library_books

Network Properties of the Ensemble of RNA Structures

2015
PLoS One
PMCID: 4619022
PMID: 26488894
DOI: 10.1371/journal.pone.0139476

[…] solute contact order for an RNA structure is defined as above. The pseudoknot (pknot) absolute contact order is defined as ∑i < j(j − i)/N, where the sum is over all N base pairs (i, j) determined by RNAview [], a program that determines hydrogen-bonded atoms of distinct nucleotides in a PDB file of RNA and additionally classifies the base pair with respect to the Leontis-Westhof classification [] […]

call_split

New in silico approach to assessing RNA secondary structures with non canonical base pairs

2015
BMC Bioinformatics
PMCID: 4557229
PMID: 26329823
DOI: 10.1186/s12859-015-0718-6
call_split See protocol

[…] driven by RNApdbee webserver []. At the input, RNApdbee accepts RNA atom coordinate data encoded in a PDB file. Next, it identifies base pairs using incorporated procedures of standalone versions of RNAView [], MC-Annotate [] or 3DNA/DSSR [], on user selection. Additional functions drive classification of non-canonical base pairs according to LW [, ] and Saenger [] nomenclatures, and identify pse […]

library_books

Effective alignment of RNA pseudoknot structures using partition function posterior log odds scores

2015
BMC Bioinformatics
PMCID: 4339682
PMID: 25727492
DOI: 10.1186/s12859-015-0464-9

[…] n such a way that they have a wide range of sequence lengths. Each three-dimensional (3D) molecule in this dataset was taken from the PDB. The secondary structure of the 3D molecule was obtained with RNAview [], retrieved from RNA STRAND. The second dataset, denoted Dataset2, contains 36 RNA pseudoknot structures chosen from PseudoBase [,] (see Additional file : Table S2). As in the first dataset, […]

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RNAView institution(s)
Department of Chemistry and Chemical Biology, Rutgers University, NJ, USA

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