Sfold protocols

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Sfold specifications

Information


Unique identifier OMICS_03468
Name Sfold
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ye Ding <>

Publication for Sfold

Sfold in pipeline

2011
PMCID: 3063221
PMID: 21388531
DOI: 10.1186/1748-7188-6-3

[…] of all intervals of an rna molecule in (n3) time and (n2) memory. this is the same complexity as the algorithm to compute the partition function, which is underlying the sampling approaches, like sfold [], commonly used for this task. however, the probabilities to be accessible for different intervals are not independent. therefore, if one is interested in more complex questions, e.g. […]


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Sfold in publications

 (113)
PMCID: 5897953
PMID: 29653577
DOI: 10.1186/s12951-018-0368-8

[…] yet to be classified. with the use of rna 2d structure prediction programme, only 70% of structure can be predicted accurately [, ]. though various online resources like mfold, 233 rna designer, 234 sfold, 235 nupack, 115 nanofolder, 236 and hyperfold, 182 have been developed, prediction of accurate rna structure and folding remains a major problem. rna 3d and 4d structure prediction is even […]

PMCID: 5852021
PMID: 29540837
DOI: 10.1038/s41598-018-22767-y

[…] that coding sequence (cds) of mrna could be directly targeted by a mirna-containing risc complex–. thus, we explored additional target genes of mir-3140 using the starmirdb database (http://sfold.wadsworth.org), which predicts mirna target genes based on cds binding. among the 228 genes downregulated by mir-3140 in 3 cell lines (fig. ), candidate binding-sites for the seed sequence […]

PMCID: 5788215
PMID: 29399550
DOI: 10.15171/apb.2017.072

[…] 3´ utr, start codon, introns and splice junctions were avoided., analyzing the internal instability, the asymmetry of sirna duplex and secondary structures of candidate sirnas were accomplished by sfold software (http://sfold.wadsworth.org). melting temperature (tm) of the sirna hairpin loop is another thermodynamic feature of sirna which was predicted by "oligoanalyzer 3.1" online service […]

PMCID: 5740175
PMID: 29269865
DOI: 10.1038/s41598-017-18326-6

[…] length and the number of snps, as described., rna folding analysis to predict the ire structure of wild-type (wt) and mutated ftl was carried out using mfold (http://unafold.rna.albany.edu/) and sfold web server (http://sfold.wadsworth.org/). rna sequences used for fold predictions are shown in supplementary table ., plasmids for generating rna probes for electrophoretic mobility shift assay […]

PMCID: 5751119
PMID: 29186809
DOI: 10.3390/ijms18122516

[…] however, difficult to handle structure prediction on the hts scale. , a recently developed platform for structure motif clustering is aptatrace []. based on the secondary structure prediction from sfold [,], aptatrace applies this information into all of the sequences input to the program. this allows for the prediction of a specific structure for each k-mer in each selection round and ranking […]


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Sfold institution(s)
Bioinformatics Center, Wadsworth Center, New York State Department of Health, Albany, NY, USA

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