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Protocols

NoFold specifications

Information


Unique identifier OMICS_20834
Name NoFold
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A file of RNA sequences
Input format FASTA
Operating system Unix/Linux
Programming languages Python, R
Computer skills Advanced
Version 1.0.1
Stability Stable
Requirements
Infernal (version including cmscore), fastcluster , LocARNA
Maintained Yes

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Documentation


Maintainers


  • person_outline Junhyong Kim
  • person_outline Sarah Middleton

Publication for NoFold

NoFold citations

 (3)
library_books

Context dependent deposition and regulation of mRNAs in P bodies

2018
eLife
PMCID: 5752201
PMID: 29297464
DOI: 10.7554/eLife.29815.043

[…] Secondary structure motifs in the 3’ untranslated regions (UTRs) of transcripts, overrepresented among differentially enriched mRNAs for each stress condition, were identified using NoFold () version 1.0. 3’ UTR sequences were extracted from the biomart project (RRID:SCR_002987) (http://biomart.org) by selecting 300 base pairs (bp) downstream of the coding sequence (CDS). The int […]

call_split

DotAligner: identification and clustering of RNA structure motifs

2017
Genome Biol
PMCID: 5747123
PMID: 29284541
DOI: 10.1186/s13059-017-1371-3
call_split See protocol

[…] ut transformation, and subjected to OPTICS clustering as implemented in the dbscan CRAN repository with a range of parameters (see Fig.  , ).Other tested RNA clustering approaches were GraphClust and NoFold. We ran GraphClust version 0.7.6 inside the Docker image provided with RNAscClust with default parameters. NoFold version 1.0.1 uses 1973 Rfam CMs by default as empirical feature space. For the […]

library_books

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

2017
Sci Rep
PMCID: 5686184
PMID: 29138457
DOI: 10.1038/s41598-017-15822-7

[…] en by REAPR and RNAz. The predicted loci in the candidate set were identified by a local BLASTN search against the Rfam database using the default parameters. The whole predicted set was clustered by NoFold into the RNA empirical structure space (RESS). The top-ranked CMs were used to rank the most similar known structures to each novel structure in the cluster. […]

Citations

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NoFold institution(s)
Genomics and Computational Biology Graduate Program, Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
NoFold funding source(s)
Supported in part by US Department of Energy (DOE) CSGF (DE-FG02-97ER25308); and National Institute of Mental Health (NIMH) 5R01MH088849 grant; and in part by a Health Research Formula Funds to Penn Genome Frontiers Institute from the Pennsylvania Department of Health.

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