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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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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

 (30)
library_books

Computational Methods for Modeling Aptamers and Designing Riboswitches

2017
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 […]

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
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 […]

library_books

A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life

2016
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 […]

library_books

High throughput identification of C/D box snoRNA targets with CLIP and RiboMeth seq

2016
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. […]

library_books

Alu retrotransposons promote differentiation of human carcinoma cells through the aryl hydrocarbon receptor

2016
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, […]

library_books

Attachment of ribosomal complexes and retrograde scanning during initiation on the Halastavi árva virus IRES

2016
PMCID: 4797288
PMID: 26783202
DOI: 10.1093/nar/gkw016

[…] in the halv 5′ utr and proximal coding sequence (genbank accession #jn000306) were modeled essentially as described (,), using probabilistic (pfold: http://www.daimi.au.dk/∼compbio/pfold/ (); and contrafold: http://contra.stanford.edu/contrafold/ ()) and posterior decoding approaches (centroidfold: http://www.ncrna.org/centroidfold ()), and were verified and refined by free energy […]


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

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