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Centroid RNA package specifications

Information


Unique identifier OMICS_03471
Name Centroid RNA package
Alternative name CentroidAlifold
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

Publications for Centroid RNA package

Centroid RNA package citations

 (5)
library_books

Computational modeling of RNA 3D structures, with the aid of experimental restraints

2014
RNA Biol
PMCID: 4152360
PMID: 24785264
DOI: 10.4161/rna.28826

[…] dynamic method or a SCFG method. Examples of thermodynamic weighting can be found in DYNALIGN and PETfold. Examples of SCFG methods include pfold. Examples of base pairing probability methods include CentroidAlifold and MXScarna. It is worth emphasizing that base-pairing may define not only secondary structure in the simplest sense, but also tertiary interactions such as pseudoknots and kissing lo […]

library_books

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

2013
Nucleic Acids Res
PMCID: 3627593
PMID: 23435231
DOI: 10.1093/nar/gkt101

[…] ok the first place in rankings generated on all RNAs from the PDB data set, regardless of whether standard or extended base pair definition was used. When the standard base pairs definition was used, CentroidAlifold(20) (CentroidAlifold run on the query sequence and 19 members of the ‘seed’ alignment from Rfam) was second and CentroidFold was third. When all base pairs from the reference secondary […]

call_split

Activity regulated RNA editing in select neuronal subfields in hippocampus

2012
Nucleic Acids Res
PMCID: 3553983
PMID: 23172290
DOI: 10.1093/nar/gks1045
call_split See protocol

[…] application in European Molecular Biology Open Software Suite (EMBOSS) using the EDNA scoring matrix and a window size of 1. The γ-centroid consensus structure was predicted from the alignment using CentroidAlifold with a default inference engine [Version 0.0.9; ()]. The common structure was superimposed onto the rat or consensus pre-mRNA sequence and visualized with Visualization Applet for RNA […]

library_books

Steric antisense inhibition of AMPA receptor Q/R editing reveals tight coupling to intronic editing sites and splicing

2012
Nucleic Acids Res
PMCID: 3553965
PMID: 23172291
DOI: 10.1093/nar/gks1044

[…] y was calculated and data output from the PLOTCON application in EMBOSS using the EDNA scoring matrix and a window size of 1. The γ-centroid consensus structure was predicted from the alignment using CentroidAlifold with a default inference engine [Version 0.0.9; ()]. The common structure was superimposed onto the rat GluA2 pre-mRNA sequence and visualized with Visualization Applet for RNA (VARNA) […]

library_books

Generalized Centroid Estimators in Bioinformatics

2011
PLoS One
PMCID: 3041832
PMID: 21365017
DOI: 10.1371/journal.pone.0016450

[…] y structure (see “Common secondary structure prediction from a multiple alignment of RNA sequences” in for detailed discussion). The representative estimator for Problem 5 is implemented in software CentroidAlifold. Another example of representative prediction is the “alignment of alignments” problem, which is the fundamental element of progressive multiple alignment of biological sequences. The […]

Citations

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Centroid RNA package institution(s)
Mizuho Information and Research Institute, Inc, Chiyoda-ku, Tokyo, Japan

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