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Protocols

CyloFold specifications

Information


Unique identifier OMICS_03454
Name CyloFold
Interface Web user interface
Restrictions to use None
Input data RNA sequence
Input format Raw, FASTA
Computer skills Basic
Maintained Yes

Maintainer


  • person_outline Bruce Shapiro

Publication for CyloFold

CyloFold citations

 (3)
call_split

Sense overlapping transcripts in IS1341 type transposase genes are functional non coding RNAs in archaea

2015
RNA Biol
PMCID: 4615843
PMID: 25806405
DOI: 10.1080/15476286.2015.1019998
call_split See protocol

[…] number of parameters in a machine learning approach; Vsfold5, which allow the prediction of pseudoknots by using sequential (5′ to 3′) folding and thermodynamically most-probable folding pathways and Cylofold, which simulates the 3D folding process in a coarse-grain model. All predictions are shown in extended dot-bracket format to include pseudoknots. All 5 methods were run using their respective […]

library_books

RNA Elements in Open Reading Frames of the Bluetongue Virus Genome Are Essential for Virus Replication

2014
PLoS One
PMCID: 3962428
PMID: 24658296
DOI: 10.1371/journal.pone.0092377

[…] (not shown). The insertions did not lead to recovery of NS3/NS3a protein expression. To examine possible similarities in RNA structure, RNA sequences were subjected to RNA structure predictions using Cylofold (http://cylofold.abcc.ncifcrf.gov/), RNASAlign (http://www.bio8.cs.hku.hk/RNASAlign/) and Alifold (http://rna.tbi.univie.ac.at/cgi-bin/RNAalifold.cgi) software. No obvious similarities in RNA […]

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

[…] . In this ranking, the other best performing methods were McQFold, Pknots and PknotsRG, which are all capable of predicting pseudoknots. As it turned out in our benchmarks, the longest RNA, for which Cylofold managed to return a prediction in our test, had 255 nt residues (ASE_00408 record from the RNAstrand data set). Because of this limit, Cylofold had only been able to generate a prediction for […]

Citations

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CyloFold institution(s)
Basic Science Program, SAIC-Frederick, Inc; NCI-Frederick, Frederick, MD; Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD, USA

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