CONTRAfold protocols

View CONTRAfold computational protocol

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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

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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 in pipelines

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

[…] expected normalized reads value was generated for each mirna based on the known abundance of the mirna in the mixture prior to library construction., rna contrafold [] (http://contra.stanford.edu/contrafold/index.html) was used for secondary structure prediction of single rna molecules using default settings. vienna rnacofold [] (http://rna.tbi.univie.ac.at/cgi-bin/rnacofold.cgi) was used […]

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

[…] sequences and 5′-constant regions were trimmed off using galaxy (). only trimmed reads that were 21 nt in length were considered in subsequent 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 […]

2010
PMCID: 2828121
PMID: 20080511
DOI: 10.1093/bioinformatics/btq014

[…] it moves along the sequence. this presents a challenge for future research., our technique does not depend on the concrete information that is accumulated for each shape. recent approaches such as contrafold (do et al., ) and cg (andronescu et al., ) replace the classical thermodynamic model by stochastic models, trained from structural data via machine learning techniques. to benefit […]


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CONTRAfold in publications

 (29)
PMCID: 5713409
PMID: 29149090
DOI: 10.3390/ijms18112442

[…] 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 […]

PMCID: 5546546
PMID: 28296577
DOI: 10.1080/15476286.2017.1306175

[…] 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 […]

PMCID: 5408919
PMID: 27993777
DOI: 10.1093/bioinformatics/btw728

[…] intramolecular structure or measures the accessibility of the binding region. there are also other machine learning algorithms (; ), and probabilistic approaches like ractip (), which uses the contrafold model () for rna interaction prediction., risearch (), bindigo () and guugle () are examples of alignment-like methods. the risearch algorithm was mainly developed for rapidly searching […]

PMCID: 5389715
PMID: 28031372
DOI: 10.1093/nar/gkw1321

[…] region in the target is in single stranded conformation within an extended region of 30 nucleotides upstream and 37 nucleotides downstream of 5΄ end of the putative site. we computed this value with contrafold ()., we defined the ‘flanks a content’ as the proportion of adenines within the 67 nts-long region defined above. we similarly computed frequencies of other nucleotides. […]

PMCID: 4889919
PMID: 26883630
DOI: 10.1093/nar/gkw095

[…] homologous to the 3′utr of nanog and significantly homologous to the 3′utr of oct4 (supplementary figure s10a and b). conditional training analysis for the prediction of rna secondary structures (contrafold) revealed the optimal conformation of nanog alu-t1 and alu-t2 transcripts in their homology regions with the 3′utr of nanog and oct4 (supplementary figure s10c and d). importantly, […]


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

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