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SeqFold specifications

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Unique identifier OMICS_08194
Name SeqFold
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, Python
Computer skills Advanced
Stability No
Maintained No

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Publication for SeqFold

SeqFold in publications

 (8)
PMCID: 5682290
PMID: 29129909
DOI: 10.1038/s41467-017-01458-8

[…] ensembles of ir alus in f11r and psmb2 differ significantly between control and kd cells with the kd samples showing fewer ds bases (wilcoxon test, p < 0.0001 for both, supplementary table ). seqfold analysis of these two examples reveal the same trend, as in both psmb2 and f11r the structures are less stable in kd conditions (δg control < δg kd)., comparison of the structural profiles […]

PMCID: 5083181
PMID: 27668660
DOI: 10.1038/ng.3673

[…] the mean intensity of highly reactive nucleotides. rna secondary structures were predicted using rna structure software (reuter et al., 2010). shape data and rna structure data were reconciled using seqfold., northern blot was performed using the northernmax kit (ambion) with 2.5–5ug of poly(a) selected rna for each sample. anti-sense rna probes to human dino nucleotides 203–716 and mouse dino […]

PMCID: 4383490
PMID: 25873772
DOI: 10.1155/2015/807976

[…] using the multiple alignment sequence profile-based searching method (psi-blast), an automated sequence and structure searching procedure (high throughput modeling), and a fold recognition method (seqfold), three-dimensional structural models of il-38 were predicted. the il-38 structural model displays a 12-β-stranded trefoil structure and shares similarity with the crystal structure of il-1ra […]

PMCID: 4152356
PMID: 24755880
DOI: 10.4161/rna.28647

[…] rnaassist formulates the problem in terms of simultaneously minimizing position-dependent energy penalties and the deviation of observed and predicted probabilities for unpaired nucleotides. seqfold uses the experimental data to select locally stable secondary structure from the boltzmann ensemble. in shapeknots, an interative procedure is used to include pseudoknots and shape […]

PMCID: 3973747
PMID: 24476892
DOI: 10.1038/nature12946

[…] (methods). we experimentally validated 9 ribosnitches using independent structure probing methods such as nucleases, shape or dms, and confirmed the ability of pars to discover ribosnitches (–). the seqfold program is used to visualize structure changes caused by ribosnitches (, )., we found 1,907 out of 12,233 (15%) snvs that switched rna structure in the trio (, , ). as ribosnitches […]


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SeqFold institution(s)
Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA

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