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TurboFold specifications


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 in publications

PMCID: 5641303
PMID: 29067038
DOI: 10.3389/fgene.2017.00147

[…] 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 […]

PMCID: 4880961
PMID: 27230657
DOI: 10.1186/s12870-016-0807-3

[…] to known mirnas and other kinds of srnas were considered un-annotated sequences for novel mirna prediction. to obtain the mirna predicted precursor structure, the sequences were analyzed by using turbofold [] http://rna.urmc.rochester.edu/rnastructure.html) and guide and star sequences were obtained., the target prediction method involved loading mirna reads in a fasta format file containing […]

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

[…] 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 […]

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., […]

PMCID: 4229120
PMID: 25391020
DOI: 10.1371/journal.pone.0112061

[…] 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., promastigotes forms of l. major lt252 (mhom/ir/1983/ir) and l. […]

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

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