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vsfold specifications

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Unique identifier OMICS_03469
Name vsfold
Interface Web user interface
Restrictions to use None
Programming languages C
Computer skills Basic
Version 5.23
Stability Stable
Maintained Yes

Publication for vsfold

vsfold citations

 (8)
library_books

Nucleotide resolution mapping of influenza A virus nucleoprotein RNA interactions reveals RNA features required for replication

2018
Nat Commun
PMCID: 5792457
PMID: 29386621
DOI: 10.1038/s41467-018-02886-w

[…] n wt-pr8 and mutant virus using vienna rnafold. all calculations were performed using the default settings without imposing structural constraints. pseudoknot formation potential was determined using vsfold5 and default settings. results for focus area, lung titer, tcid50 ml−1:ha ratio, relative segment packaging are summarized from previous figures (=, equivalent to wt-pr8; ↓, p < 0.05; ↓↓, p  […]

library_books

CRISPR/Cas9 editing reveals novel mechanisms of clustered microRNA regulation and function

2017
Sci Rep
PMCID: 5561095
PMID: 28819307
DOI: 10.1038/s41598-017-09268-0

[…] ed by rnafold (vienna rna tools, http://rna.tbi.univie.ac.at/cgi-bin/rnawebsuite/rnafold.cgi) using the turner model (standard settings), while secondary structures with pseudoknots were generated by vsfold5 (chiba institute of technology, japan, http://www.rna.it-chiba.ac.jp/~vsfold/vsfold5/) and settings: 37 °c temperature; kuhn length 6; jacobson-stockmayer gamma = 1.75 and contiguous stems = 6 […]

library_books

An improved method for identification of small non coding RNAs in bacteria using support vector machine

2017
Sci Rep
PMCID: 5382675
PMID: 28383059
DOI: 10.1038/srep46070

[…] been introduced over the years to identify srnas of bacteria, but most of them show poor performance in identifying positive and negative srnas simultaneously. thus, methods such as msari, rnaz2, vsfold, alifoldz and dynalign showed good performance in identifying negative srnas (non-srnas) identification, but poor ability in identifying positive srnas (). on the other hand, zmfold […]

library_books

Survey of Natural Language Processing Techniques in Bioinformatics

2015
PMCID: 4615216
PMID: 26525745
DOI: 10.1155/2015/674296

[…] the predictions [], which are similar to the text mining techniques., because of the importance of rna structure, several computational rna folding tools have been developed, such as mfold, rnafold, vsfold, evofold, and sfold. generally, these algorithms determine the folded secondary structure from and input sequence by optimizing the intermolecular base pairing to minimize the free energy. […]

library_books

Sense overlapping transcripts in IS1341 type transposase genes are functional non coding RNAs in archaea

2015
RNA Biol
PMCID: 4615843
PMID: 25806405
DOI: 10.1080/15476286.2015.1019998

[…] the minimum free energy (mfe) structure; rnafold using thermodynamic partition function centroids algorithm; contextfold, which uses a very large number of parameters in a machine learning approach; vsfold5, which allow the prediction of pseudoknots by using sequential (5′ to 3′) folding and thermodynamically most-probable folding pathways and cylofold, which simulates the 3d folding process […]

library_books

Incomplete concerted evolution and reproductive isolation at the rDNA locus uncovers nine cryptic species within Anopheles longirostris from Papua New Guinea

2010
BMC Evol Biol
PMCID: 3022607
PMID: 21184676
DOI: 10.1186/1471-2148-10-392

[…] as compensatory. additionally, the issue of compensatory base changes within rna pseudoknots also seemed unlikely but could not be fully explored due to the 450 bp sequence length limits of the vsfold5 pseudoknot prediction software []. however, as the its2 sequence folded consistently 5' to 3' in mfold we could utilize partial sequences in the pseudoknot analyses. nevertheless, we found […]


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vsfold institution(s)
Chiba Institute of Technology, Tsudanuma, Narashino-shi, Chiba, Japan; International Medical Center of Japan, Toyama, Shinjuku-ku, Tokyo, Japan
vsfold funding source(s)
Supported by a grant-in-aid for high technology research from the ministry of Education, Science, Sports and Culture, Japan.

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