COFOLD protocols

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COFOLD specifications

Information


Unique identifier OMICS_09291
Name COFOLD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Irmtraud M. Meyer <>

Information


Unique identifier OMICS_09291
Name COFOLD
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Irmtraud M. Meyer <>

Publication for COFOLD

COFOLD in pipelines

 (3)
2015
PMCID: 4420488
PMID: 25942392
DOI: 10.1371/journal.pone.0126049

[…] the formation of stem(s) and loop(s) and the relative position of the a-b junction in the loop or stem structure, all the secondary structures of ab were classified into 16 categories (). the same cofold analysis was applied to the randomized 5’ adaptors (molecule a) and the mirna-3’adaptor combined sequences (molecule b). the rna cofold batch analysis pipeline was written in custom perl […]

2015
PMCID: 4737167
PMID: 26704983
DOI: 10.1093/nar/gkv1488

[…] assuming that transcription was initiated at one of the single-stranded loops. the minimum free energy (mfe) and co-transcriptionally folded structures were determined using the rnafold () and cofold () web servers, respectively. both predictions were carried out using the energy/folding parameters indicated in the text. 3d models based on mfe or co-transcriptional folding were generated […]

2012
PMCID: 3326334
PMID: 22241775
DOI: 10.1093/nar/gkr1263

[…] analyses. rna contrafold (http://contra.stanford.edu/contrafold/index.html) was used for rna secondary structure prediction. default settings were used for the prediction. to predict rna and adapter cofold structures, the vienna rnacofold (http://rna.tbi.univie.ac.at/cgi-bin/rnacofold.cgi) was used with the default setting of minimum free energy algorithms and folding temperature at 25°c (,). […]


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COFOLD in publications

 (16)
PMCID: 5896230
PMID: 29590610
DOI: 10.1016/j.celrep.2018.03.018

[…] and pathway analysis are described in detail in , as is the validation of degs using qrt-pcr., genome-wide in silico prediction of snord116 targets was performed using snotarget software () and rna-cofold from the vienna rna package (http://www.tbi.univie.ac.at/rna/)., reference gene sets for broad neuronal subtype classifications were derived from as described in . reference gene sets […]

PMCID: 5850609
PMID: 29220489
DOI: 10.1093/molbev/msx310

[…] particular motifs, we evaluate the hybridization energy between each eight nucleotide segment contained within the −20 to −4 region and the putative asd sequence defined as 5′-accuccuu-3′ using the “cofold” method of the viennarna software package with default parameters. if any sequence binds at a threshold of −4.5 kcal/mol or stronger (i.e., more negative δg values), we consider this gene […]

PMCID: 5713409
PMID: 29149090
DOI: 10.3390/ijms18112442

[…] be used to study the large scale conformational fluctuations of rnas., also based on the coarse-grained structural model, a number of computational methods, such as rnakinetics [], kinefold [], and cofold [] are developed to simulate co-transcriptional folding pathways of mrnas from the early 1980s when key experiments show that structure formation happens co-transcriptionally []. in order […]

PMCID: 5406134
PMID: 28508050
DOI: 10.1126/sciadv.1603119

[…] chiral imbalance is a further indication of the validity of a cofolding scenario where the chiral nature of chitin () can be the cause of the chiral imbalance of the formed nanostructures (in the cofold scenario, chitin is present during the gyroid formation stage). the observed faceting of the crystallites is consistent with both growth models because it has been observed […]

PMCID: 5100845
PMID: 27605518
DOI: 10.1534/g3.116.032227

[…] real genome along with the resulting p value, which we report in the main text., we predicted thermodynamic interactions between the asd sequence and each six-nucleotide-long sequence using the rna cofold method of the viennarna package 2.0 with default parameters (). for this study, we have chosen to use the canonical core asd sequence of 5′-ccuccu-3′ for all species, owing to the fact […]


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COFOLD institution(s)
Centre for High-Throughput Biology, University of British Columbia, East Mall, Vancouver, BC, Canada; Department of Computer Science, University of British Columbia, East Mall, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, East Mall, Vancouver, BC, Canada

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