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RNAsubopt specifications

Information


Unique identifier OMICS_26215
Name RNAsubopt
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.4.3
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Walter Fontana

Publication for RNAsubopt

RNAsubopt citations

 (58)
library_books

Aptamer Bioinformatics

2017
Int J Mol Sci
PMCID: 5751119
PMID: 29186809
DOI: 10.3390/ijms18122516

[…] k-mer in each selection round and ranking by predicted significant structural enrichment. APTANI is a similar program, able to cluster sequence motifs based on secondary structure prediction. It uses RNAsubopt from the Vienna RNA package [] and predicts using sub-structures, apical loops, bulge loops, and intra-strand loops. This method was validated using a SELEX against IL4Ra. Using APTANI, an a […]

call_split

Computational Methods for Modeling Aptamers and Designing Riboswitches

2017
Int J Mol Sci
PMCID: 5713409
PMID: 29149090
DOI: 10.3390/ijms18112442
call_split See protocol

[…] 2D structure (e.g., RNAfold []), only find the structure with the lowest free energy for a given RNA. As the functional structure may not be the one with the lowest energy, methods such as mfold and RNAsubopt [,] are developed to predict a set of low-energy structures. Other prediction methods, such as PPfold and RNAalifold [,], are based on evolutionary considerations. For a given aptamer, these […]

library_books

RNA editing by ADAR1 leads to context dependent transcriptome wide changes in RNA secondary structure

2017
Nat Commun
PMCID: 5682290
PMID: 29129909
DOI: 10.1038/s41467-017-01458-8

[…] were done using RNAplot of Vienna package. R-chie was used to draw the arc diagrams of the RNA 2D structures (as in Fig. ).In order to compare structural ensembles in control and KD samples, we used RNAsubopt of Vienna package with 1000 random suboptimal structures using constrains derived from our PARS-seq experiment (RNAsubopt –p 1000 –C).Selected examples (e.g., the F11R and PSMB2 IR Alu regio […]

library_books

Tractable RNA–ligand interaction kinetics

2017
BMC Bioinformatics
PMCID: 5657077
PMID: 29072147
DOI: 10.1186/s12859-017-1823-5

[…] y a selected part of all possible secondary structures of the input RNA. For this work, we consider only structures up to a certain energy above the minimum free energy of the sequence as computed by RNAsubopt []. To further reduce the number of structures, only structures without any isolated base pairs are generated.Often, the restriction to low energy structures excludes important microstates o […]

library_books

Detecting and characterizing microRNAs of diverse genomic origins via miRvial

2017
Nucleic Acids Res
PMCID: 5716067
PMID: 29036674
DOI: 10.1093/nar/gkx834

[…] tructures of the (merged) loci were obtained by a RNA-fold program such as RNAfold in the ViennaRNA package () or Mfold (). miRvial could parse and analyze multiple secondary structures. For example, RNAsubopt can generate suboptimal secondary structures within a user-defined range. miRvial considers all of the structures from the folding program and search for miRNAs with alternative suboptimal s […]

library_books

Ribosome signatures aid bacterial translation initiation site identification

2017
BMC Biol
PMCID: 5576327
PMID: 28854918
DOI: 10.1186/s12915-017-0416-0

[…] ntified as sequences predicted to have a binding energy with the anti-SD sequence (AGGAGGTG) of –8 kcal/mol or lower. Energies were calculated in 8 nt overlapping windows across the whole genome with RNAsubopt (version 2.1.9) [], and assigned to the first “A” of the anti-SD sequence. Upstream SD sequences were defined as those within 30 nt upstream of an annotated start codon. Downstream SD sequen […]

Citations

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RNAsubopt institution(s)
Institut fur Theoretische Chemie, Universitat Wien, Wien, Austria; Santa Fe Institute, Santa Fe, NM, USA
RNAsubopt funding source(s)
Supported by Austrian Fond zur Forderung der Wissenschaftlichen Forschung (FWF) and Santa Fe Institute Contract grant number: 11065-CHE (FWF).

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