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StructureFold specifications

Information


Unique identifier OMICS_08191
Name StructureFold
Interface Web user interface
Restrictions to use None
Input format FASTA, FASTQ
Computer skills Basic
Stability Stable
Maintained Yes

Publication for StructureFold

StructureFold in publications

 (2)
PMCID: 5909432
PMID: 29373706
DOI: 10.1093/nar/gky036

[…] was performed as previously described () using the chemmodseq pipeline (https://bitbucket.org/sgrann/chemmodseqpipeline). the resulting data were then used to calculate shape reactivities using the structurefold () and bum-hmm () algorithms. the shape reactivities were subsequently scaled using a 2–8% normalization step (). to compare shape reactivities between δ5 and δerb1 we used the raw […]

PMCID: 5620067
PMID: 28959008
DOI: 10.1038/s41467-017-00761-8

[…] of nucleotides modified compared to our shape reactivity script, which is why we decided not to use it for these analyses. in this manuscript, we calculated shape reactivities according to the structurefold method using the calculateshape_reactivities.py script., the chemmodseq pipeline first trims the adapter sequences from the reads using flexbar followed by demultiplexing of the samples […]


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StructureFold institution(s)
Department of Biology, Center for RNA Molecular Biology, Bioinformatics and Genomics Graduate Program,Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA; Galaxyprojectorg, University Park, PA, USA and Baltimore, MD, USA

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