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TurboFold specifications

Information


Unique identifier OMICS_03482
Name TurboFold
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for TurboFold

TurboFold citations

 (9)
library_books

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

[…] File in sections (a) and (b), respectively.RNAfold and CentroidHomfold (used for single sequence prediction) tended to pair the sequences of long single-strand segments (Figures ). More accurate was Turbofold thanks to all the sequences of the homologs used as input (Figure ). Locarna and the refold.pl-based method that used the experimentally identified structure as constraint did not predict pl […]

call_split

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs

2017
Nucleic Acids Res
PMCID: 5714223
PMID: 29036420
DOI: 10.1093/nar/gkx815
call_split See protocol

[…] h and for values 0, 0.6, 0.8, 1.0, 2.0, 3.0, 4.0, and 5.0, and for values 0, 0.3, 0.5, 0.7 and 1.0. The resulting optimal parameters ( = 1.0, = 0.8, = 0.5) were then used as the defaults for the TurboFold II. illustrates the landscape for the grid search. The HMM parameters and the alignment constraint thresholds (the cutoff value below which co-incidence probabilities were excluded from the […]

library_books

Genome wide identification of microRNAs in pomegranate (Punica granatum L.) by high throughput sequencing

2016
BMC Plant Biol
PMCID: 4880961
PMID: 27230657
DOI: 10.1186/s12870-016-0807-3

[…] NA precursors of Japanese apricot []. Among 10 miRNAs, 6 had a 5’ arm and 4 had a 3’ arm. The stem loop structures of predicted novel miRNA candidates were drawn from the precursor sequences by using TurboFold (Fig. ) [].Fig. 4Novel miRNA prediction was summarized as the base bias on the first position from the 5’ end and base bias on each position (Fig. ). With the exception of 18 nt for 18- to 2 […]

library_books

RNA folding with hard and soft constraints

2016
PMCID: 4842303
PMID: 27110276
DOI: 10.1186/s13015-016-0070-z

[…] tion from aligned RNA sequences. Here sequence covariation supporting base pairs is rewarded by a small additional stabilizing pseudo-energy [, ]. A similar approach has been pursued more recently in TurboFold [].Soft constraints have gained considerable interest in the analysis of chemical and enzymatic probing experiments. In RNAstructure [–], SHAPE reactivities are converted to position-specifi […]

library_books

Placenta Enriched LincRNAs MIR503HG and LINC00629 Decrease Migration and Invasion Potential of JEG 3 Cell Line

2016
PLoS One
PMCID: 4833476
PMID: 27023770
DOI: 10.1371/journal.pone.0151560

[…] were compared to the studied genes and further aligned to the human genome, through the BLAT tool [] (website: http://genome.ucsc.edu/). Additionally, we predicted the common RNA structure using the TurboFold algorithm, available in RNAstructure platform (http://rna.urmc.rochester.edu/RNAstructureWeb/) [], which presents the common RNA structures with the lowest free energy values. […]

call_split

The Putative Leishmania Telomerase RNA (LeishTER) Undergoes Trans Splicing and Contains a Conserved Template Sequence

2014
PLoS One
PMCID: 4229120
PMID: 25391020
DOI: 10.1371/journal.pone.0112061
call_split See protocol

[…] mania species analyzed, and then the constraints from the consensus structure were applied to the individual TER modeling by the execution of mfold with default parameters . Pknots , KnotSeeker , and Turbofold algorithms were applied without any success in our attempt to detect pseudoknots along the entire Leishmania TER sequences. […]

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TurboFold institution(s)
Department of Electrical and Computer Engineering, University of Rochester, Chinahester, NY, USA

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