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Protocols

CompaRNA specifications

Information


Unique identifier OMICS_15809
Name CompaRNA
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Tomasz Puton

Publication for CompaRNA

CompaRNA citations

 (5)
call_split

Impact of the structural integrity of the three way junction of adenovirus VAI RNA on PKR inhibition

2017
PLoS One
PMCID: 5650172
PMID: 29053745
DOI: 10.1371/journal.pone.0186849
call_split See protocol

[…] Secondary structures were predicted for wt and mutant RNA mutants using ContextFold [], a program that scored one of the most accurate single-sequence RNA structure predictions according to the CompaRNA benchmark []. In all cases but one, the effects of deletions on secondary structure were local, while in the Δ4bp variant, the deletion of the helix core has led to a rearrangement of the 3wj […]

library_books

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

[…] they can be regarded as true positives (Table ). An additional experiment performed to potentially distinguish between true and false positives has been performed on the benchmark set available from CompaRNA website []. We have compared predicted models to reference structures, which were derived for RNAs with experimentally determined atom coordinates (Additional file : Table S3). By computing p […]

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

[…] fold and align two or multiple RNA sequences considering pseudoknots without known structures. Similar techniques were implemented in DAFS [] and SimulFold []. Additional methods can be found in the CompaRNA web server []. In contrast to these methods, which perform alignment and folding at the same time, RKalign aims to align two known RNA pseudoknot structures where the structures are obtained […]

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

[…] ments) was insufficient for a statistically meaningful evaluation at the time of writing of this manuscript. Rankings generated on the PDB data sets will be automatically updated and presented on the CompaRNA website, while new RNA structures appear in the PDB database, hopefully allowing for a statistically significant evaluation of more methods in the future. […]

library_books

RNA and protein 3D structure modeling: similarities and differences

2011
J Mol Model
PMCID: 3168752
PMID: 21258831
DOI: 10.1007/s00894-010-0951-x

[…] ilar to Livebench (again, an inspiration from the field of protein structural bioinformatics), which aims to become an objective benchmark of fully automated methods for RNA structure prediction. The CompaRNA web server (http://comparna.amu.edu.pl, T.P., K.R., Łukasz Kozłowski, Ewa Tkalińska, J.M.B., manuscript in preparation) provides a continuous benchmark for standalone and web server methods. […]

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CompaRNA funding source(s)
This work was supported by the European Research Council (ERC, StG grant RNA+P=123D), the Polish Ministry of Science and Higher Education (currently National Science Center (NCN), grant N N301 035539), European Social Fund (‘Scholarship support for PhD students specializing in majors strategic for Wielkopolska’s development’, Sub-measure 8.2.2 Human Capital Operational Programme, co-financed by European Union under the European Social Fund), the Deutscher Akademischer Austauschdienst (D/09/42768), and an ‘Ideas for Poland’ fellowship from the Foundation for Polish Science.

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