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Protocols

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 citations

 (18)
call_split

A Transcriptomic Signature of the Hypothalamic Response to Fasting and BDNF Deficiency in Prader Willi Syndrome

2018
Cell Rep
PMCID: 5896230
PMID: 29590610
DOI: 10.1016/j.celrep.2018.03.018
call_split See protocol

[…] 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/). […]

library_books

Capturing the ‘ome’: the expanding molecular toolbox for RNA and DNA library construction

2018
Nucleic Acids Res
PMCID: 5888575
PMID: 29514322
DOI: 10.1093/nar/gky167

[…] ed to primary sequence preferences, it has become clear that the structural properties of the RNA substrate, the adaptor and the propensity of substrate and adaptor to form stimulating or inhibitory ‘cofold’ structures, control the efficiency of ligation at both sides, although the role of different structure classes differ for 3′ end and 5′ end (,,). An exhaustive investigation has further reveal […]

library_books

Diversity of Translation Initiation Mechanisms across Bacterial Species Is Driven by Environmental Conditions and Growth Demands

2017
Mol Biol Evol
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 to be […]

library_books

Computational Methods for Modeling Aptamers and Designing Riboswitches

2017
Int J Mol Sci
PMCID: 5713409
PMID: 29149090
DOI: 10.3390/ijms18112442

[…] can 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 to in […]

library_books

Butterfly gyroid nanostructures as a time frozen glimpse of intracellular membrane development

2017
Sci Adv
PMCID: 5406134
PMID: 28508050
DOI: 10.1126/sciadv.1603119

[…] his 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 in both membrane-tem […]

library_books

Depletion of Shine Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent

2016
PMCID: 5100845
PMID: 27605518
DOI: 10.1534/g3.116.032227

[…] 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 that thi […]


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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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