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SeqFold specifications

Information


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 citations

 (9)
library_books

RNA editing by ADAR1 leads to context dependent transcriptome wide changes in RNA secondary structure

2017
Nat Commun
PMCID: 5682290
PMID: 29129909
DOI: 10.1038/s41467-017-01458-8

[…] end of the normalization step the sum of all read starts in each sample was equal. To classify bases as DS or SS or undetermined class (typically low coverage regions), we used the pars2spp script of SeqFold package. This script gets the counts of read starts at each position and outputs the secondary structure class (DS or SS), employing Fisher exact test to assess significance. We ran this proce […]

library_books

An inducible long noncoding RNA amplifies DNA damage signaling

2016
Nat Genet
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. […]

library_books

Role of IL 38 and Its Related Cytokines in Inflammation

2015
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 […]

library_books

Bioinformatics of prokaryotic RNAs

2014
RNA Biol
PMCID: 4152356
PMID: 24755880
DOI: 10.4161/rna.28647

[…] pproach. 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 information […]

library_books

Landscape and variation of RNA secondary structure across the human transcriptome

2014
Nature
PMCID: 3973747
PMID: 24476892
DOI: 10.1038/nature12946

[…] For each SNV we used SeqFold to predict RNA secondary structure for a transcript fragment of 151 nucleotides (50 nucleotides upstream to 100 nucleotides downstream of the SNV sites). We used the PARS scores from allele sp […]

library_books

Tackling Structures of Long Noncoding RNAs

2013
Int J Mol Sci
PMCID: 3876070
PMID: 24304541
DOI: 10.3390/ijms141223672

[…] udies of the transcriptome (discussed below) are in need of tools capable of analyzing thousands of transcripts simultaneously, while at the same time being robust to sparse sampling. The integrative SeqFold package has been developed to tackle the RNA structurome. This package is based on Boltzman-weighted sampling to decrease the sensitivity to noise []. It has been adapted to handle the diverse […]


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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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