RNAfold pipeline

RNAfold specifications

Information


Unique identifier OMICS_03464
Name RNAfold
Interface Web user interface
Restrictions to use None
Input data DNA or RNA sequence
Input format FASTA
Programming languages C
Computer skills Basic
Stability Stable
Maintained Yes

Publications for RNAfold

library_books

CUDA RNAfold.

2018 BioRxiv
DOI: 10.1101/298885

RNAfold IN pipelines

 (4)
2012
PMCID: 3303730
PMID: 22369626
DOI: 10.1186/1471-2164-13-S1-S14

[…] 4000. mathuriya et al. [15] present their parallel implementation of gtfold on a 32-core ibm p5-570 server and 19.8 speedup is achieved. on multi-core processor, wu et al. [16] parallelized the rnafold program on quad-core intel q6600 processor to obtain 3.88 speedup. another solution to accelerate the zuker algorithm is to use accelerators. based on the fpga platform, dou et al. [17] […]

2011
PMCID: 3152330
PMID: 21478170
DOI: 10.1093/nar/gkr168

[…] all the annotated coding sequences from the m. tuberculosis cdc1551 complete genome and extracted subsequences from โˆ’20 to +80โ€‰nt around all annotated gene termini. these were each folded using the rnafold routine from the vienna package (39) and then subjected to a permutation test, where native minimum free energies (mfes) were compared to the pooled distribution of mfes for 1000 permuted […]

2010
PMCID: 2934861
PMID: 20802494
DOI: 10.1038/nnano.2010.160

[…] is the weighted sum of three scores: (i) a rule-based score35,36, (ii) a score comparing the target secondary structure with rnacofold37โ€“39 predictions of all sequence pairs as well as with rnafold37,40 predictions of all individual sequences, and (iii) a score evaluating a multi-sequence secondary structure prediction based on a trivial energy model34. three different cube types […]

2007
PMCID: 1950533
PMID: 17586815
DOI: 10.1093/nar/gkm474

[…] at http://lowelab.ucsc.edu/snoscan/). however, the c-box scoring function was modified so that it read user-specified input of the c-box scoring matrix., rna structures were generated using the rnafold program from the vienna-rna-1.4 package (http://www.tbi.univie.ac.at/~ivo/rna/windoze/), structural alignment was done using rsmatch1.0 converted for windows (original program is available […]

RNAfold institution(s)
University of Vienna-Institute of Theoretical Chemistry, Vienna, Austria

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