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Citations per year

Number of citations per year for the bioinformatics software tool CONTRAfold
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This map represents all the scientific publications referring to CONTRAfold per scientific context
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Protocols

CONTRAfold specifications

Information


Unique identifier OMICS_03452
Name CONTRAfold
Alternative name CONTRA-fold
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Information


Unique identifier OMICS_03452
Name CONTRAfold
Alternative name CONTRA-fold
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for CONTRAfold

CONTRAfold citations

 (40)
library_books

RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model

2018
PLoS One
PMCID: 5886407
PMID: 29621250
DOI: 10.1371/journal.pone.0194583

[…] dicted by HotKnots V2.0 (out of up to 20 structures predicted for each sequence) as the structure predicted by HotKnots to compare with other methods.We ran IPknot with no refinement, scoring model = Contrafold, level = 2, and γ1 = 4 and γ2 = 16, as it yields the best results. […]

library_books

A new yeti crab phylogeny: Vent origins with indications of regional extinction in the East Pacific

2018
PLoS One
PMCID: 5856415
PMID: 29547631
DOI: 10.1371/journal.pone.0194696

[…] s alignment tool in Geneious Pro 6.1.8 and ribosomal genes (16S, 28S, and 18S) were aligned using the online version of MAFFT 7.309 []. For all three ribosomal genes, the X-INSi framework [] with the CONTRAfold algorithm [] was used, which incorporates predicted secondary structure. Alignments were then adjusted by eye. Highly variable regions in the rRNA fragments that were hard to align were exc […]

call_split

Computational Methods for Modeling Aptamers and Designing Riboswitches

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

[…] ots and higher order structures, respectively. Although the input RNA 2D structure can be obtained by using the methods that are incorporated within the RNAComposer system: RNAfold, RNAstructure, and Contrafold, experimentally adjusted 2D structure is able to largely improve quality of the prediction [].The input RNA 2D structure first is divided into stems, loops, and single strands in the progra […]

call_split

Differential degeneration of the ACTAGT sequence among Salmonella: a reflection of distinct nucleotide amelioration patterns during bacterial divergence

2017
Sci Rep
PMCID: 5591236
PMID: 28887484
DOI: 10.1038/s41598-017-11226-9
call_split See protocol

[…] om stdin, calculates their minimum free energy (mfe) structure and prints to stdout. We used the mountain.pl script to produce mountain plots and the Maximum Expected Accuracy method with the program CONTRAfold to predict the pseudo-knot-free structures. CONTRAfold uses the maximum P (i, j) expected accuracy approach for the predictions. We also used RNAstructure (Mathews Lab, University of Roches […]

library_books

Genome wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA

2017
RNA Biol
PMCID: 5546546
PMID: 28296577
DOI: 10.1080/15476286.2017.1306175

[…] off of 1E-3 was used to identify RNAcentral matches for each putative sRNA. If an sRNA had multiple RNAcentral matches only the most significant match was considered. CentroidFold with parameters -e “CONTRAfold” and -g 4 was used to predict the secondary structure of putative sRNAs and random genomic sequences. Sequences of the sRNAs including 150 nts upstream of the predicted 5′ end were obtained […]

call_split

Conserved intergenic sequences revealed by CTAG profiling in Salmonella: thermodynamic modeling for function prediction

2017
Sci Rep
PMCID: 5337935
PMID: 28262684
DOI: 10.1038/srep43565
call_split See protocol

[…] y low entropy. By superimposing several mountain plots, the structures can easily be compared.To test the reliability of the modeling, we also used the Maximum Expected Accuracy method by the program CONTRAfold and predicted the most probable structure and the pseudo-knot-free structures by maximizing the sum of the base-paired and single-stranded nucleotide probabilities, called expected accuracy […]


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CONTRAfold institution(s)
Computer Science Department, Stanford University, Stanford, CA, USA

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