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vsfold specifications

Information


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

[…] nal nucleotide of each regionm, where Q ≤ 0.1. These areas represent low-NP or high-NP-binding regions of interest (ROI). ROI ≥ 18 nt were subjected to RNA structure analysis with mFold, RNAfold, and vsFold5 to determine computationally the theoretical minimal free energy (ΔG) of each region as well as the potential secondary or tertiary RNA structure formation,. Nucleotide composition of ROIs was […]

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

[…] nha University, S Korea http://wilab.inha.ac.kr/pseudoviewer/). The RNAComposer (Poland, http://rnacomposer.cs.put.poznan.pl/) was used to generate the pbd-files through molecular RNA simulation from vsfold5 output. The RNAComposer output pdb-files were then input to pyMOL to generate high quality 3D images. MiR-497a stem loop is depicted in green and its’ terminal loop in magenta. MiR-195a stem l […]

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

[…] ave 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 was efficie […]

call_split

Survey of Natural Language Processing Techniques in Bioinformatics

2015
PMCID: 4615216
PMID: 26525745
DOI: 10.1155/2015/674296
call_split See protocol

[…] ke 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. Some […]

call_split

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
call_split See protocol

[…] 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 in a […]

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

[…] th optimal and suboptimal structures were generated and observed for compensatory base changes. Additionally, the issue of compensatory base changes within RNA pseudoknots was also investigated using vsfold5 pseudoknot prediction software []. Limitations in the software (maximum sequence length is 450 bp) only permitted the analysis of partial ITS2 sequences and these were derived from nucleotide […]

Citations

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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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