Tool stats & trends
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|Interface||Web user interface|
|Restrictions to use||None|
|Input data||RNA sequence|
|Input format||Raw, FASTA|
- person_outline Bruce Shapiro
Publication for CyloFold
Sense overlapping transcripts in IS1341 type transposase genes are functional non coding RNAs in archaea
[…] 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 […]
RNA Elements in Open Reading Frames of the Bluetongue Virus Genome Are Essential for Virus Replication
[…] (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 […]
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction
[…] . 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 […]
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