RNAup protocols

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RNAup specifications

Information


Unique identifier OMICS_09346
Name RNAup
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.1.9
Stability Stable
Maintained Yes

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  • person_outline RNAinverse <>

Publication for RNAup

RNAup in pipelines

 (2)
2017
PMCID: 5621056
PMID: 28867802
DOI: 10.3390/s17091990

[…] has a high probability to be unpaired and shows a particular sequence pattern; a prominent example is the rbs. the probability that a certain sequence interval is unpaired can be computed e.g., with rnaup [,] or intarna []. the probability that a particular sequence motif is present in a structural context, e.g., partially structured binding site in the equilibrium ensemble, can also be obtained […]

2011
PMCID: 3063221
PMID: 21388531
DOI: 10.1186/1748-7188-6-3

[…] the joint probability that two intervals are accessible, this is no way around sampling the structures of the molecules., the first predecessor of our algorithm, not yet fully (n3), has been used in rnaup []. the rnaplfold program of the viennarna package [] originally used the algorithm introduced in [], but has been rewritten to use the efficient version of the algorithm presented below., […]


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RNAup in publications

 (42)
PMCID: 5459991
PMID: 28555645
DOI: 10.1038/ncomms15622

[…] of the hairpin to unwind and allow access to the isomir-4534 by strand invasion (). the target accessibility and binding energy for the isomir-4534-parna interaction were further estimated using rnaup. consistently, the energy requirements for both unwinding of the target (9.6 versus 12.0 kcal mol−1) and isomir-4534 binding (−7.8 versus −5.4 kcal mol−1) indicate greater accessibility […]

PMCID: 5831936
PMID: 29657288
DOI: 10.3390/ncrna3020017

[…] greater than the threshold. we used the default cutoff threshold of 3.0. we also identified target accessibility as the maximum energy to unpair the target site (upe). the psrnatarget server employs rnaup to calculate target accessibility, represented by the energy required to open (unpair) the secondary structure from around the target site. the lower the energy score, the greater […]

PMCID: 5357899
PMID: 28317874
DOI: 10.1038/srep44836

[…] site in sirna δgs and mrna δgm. the second component describes the energy gained by sirna-mrna interaction δgh. we can obtain the three thermodynamic parameters using a simple web server tool rnaup developed by mückstein u in university of vienna. the tool only needs the sequences of sirna and targeted mrna, and will output the three thermodynamic parameters soon. we use rnaup […]

PMCID: 5354610
PMID: 28327787
DOI: 10.1590/0074-02760160404

[…] we then wondered whether the mir-744 and mir-484 binding sites on the 3′ utr of denv rna () are accessible in the presence of the sl and hairpin. using the rnaup webserver (http://rna.tbi.univie.ac.at/cgi-bin/rnawebsuite/rnaup.cgi) we found that the total free energy of the mir-484-3′ utr was -8.92 kcal/mol with an opening energy (accessibility) of 5.16 […]

PMCID: 5435917
PMID: 28334800
DOI: 10.1093/nar/gkx115

[…] neglecting intramolecular structure (e.g. rnaduplex (), rnahybrid (), targetrna () and rnaplex ()) to (ii) those considering only one interaction site and intramolecular structure (e.g. nupack (), rnaup (), accessfold () and intarna ()), or even to (iii) those highly computationally complex tools that predict several interactions sites (e.g. iris ()) and the joint rna–rna secondary structure […]


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RNAup institution(s)
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria

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