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CentroidHomfold specifications

Information


Unique identifier OMICS_03450
Name CentroidHomfold
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_03450
Name CentroidHomfold
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for CentroidHomfold

CentroidHomfold citations

 (3)
call_split

An Algorithm for Template Based Prediction of Secondary Structures of Individual RNA Sequences

2017
Front Genet
PMCID: 5641303
PMID: 29067038
DOI: 10.3389/fgene.2017.00147
call_split See protocol

[…] les S2, S3. The sequences are included in Supplementary File . Templates including their sequences and structures are included in Supplementary File . The dataset was created from the test dataset of CentroidHomfold (Kiryu et al., ; Hamada et al., ) and extended with other RNAs to get more sequence/structure variability. The dataset consisted of 32 RNA families where at least one experimentally id […]

library_books

A general approach to high yield biosynthesis of chimeric RNAs bearing various types of functional small RNAs for broad applications

2015
Nucleic Acids Res
PMCID: 4402540
PMID: 25800741
DOI: 10.1093/nar/gkv228

[…] The secondary structures of chimeric ncRNAs were predicted using the CentroidFold (http://www.ncrna.org/centroidfold) () and CentroidHomfold (http://www.ncrna.org/centroidhomfold) (). […]

library_books

Generalized Centroid Estimators in Bioinformatics

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

[…] RNA sequences and is the length of RNA sequences. In , we employed a further approximation of the estimator, and reduced the computational cost to . We implemented this estimator in software called CentroidHomfold. See for details of the theory and results of computational experiments. Although the authors did not mention it in their paper , the following property holds.Property 19 (Computation […]

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CentroidHomfold institution(s)
Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan

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