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IPknot specifications

Information


Unique identifier OMICS_03457
Name IPknot
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

Maintainer


  • person_outline Kengo Sato

Information


Unique identifier OMICS_03457
Name IPknot
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Kengo Sato

Publication for IPknot

IPknot citations

 (9)
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

[…] By comparing four of the best methods for prediction of RNA pseudoknotted secondary structure (i.e. IPknot, a method based on maximum expected accuracy, HotKnots, a heuristic method, CCJ, a method based on MFE, and Iterative HFold, a method based on relaxed hierarchical folding hypothesis), while th […]

library_books

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools

2018
Front Genet
PMCID: 5780412
PMID: 29403526
DOI: 10.3389/fgene.2017.00231

[…] nt and allows multiple alignments of RNA sequences in ClustalW format or multiple FASTA formats to predict their consensus secondary structure. IPknot is available at http://rtips.dna.bio.keio.ac.jp/ipknot/. […]

library_books

Structure Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA

2017
Viruses
PMCID: 5454406
PMID: 28445416
DOI: 10.3390/v9050093

[…] dynamically stable tertiary interaction within the Ty1 RNA. This conclusion is supported by the fact that other RNA structure prediction algorithms that do not employ SHAPE data, such as pknotsRG and IPknot [,], also predict a pseudoknot with identical S1 and S2 stems and L2 nucleotide in the 5′ leader of Ty1 RNA ().The multibranched L1 loop (8/254) of the pseudoknot, formed by stem S1, contains t […]

library_books

Mammalian Mitochondrial ncRNA Database

2015
Bioinformation
PMCID: 4748022
PMID: 26912953
DOI: 10.6026/97320630011512

[…] ript. From the extracted non-coding regions, the representative ncRNAs have been identified using the program RNAcon []. Further, secondary structures were generated for all the predicted ncRNA using ipKnot [] and viewed using VARNA software []. The database has been developed and configured using LAMP (Linux, Apache, MySQL, and PHP) server. […]

library_books

Messenger RNAs bearing tRNA like features exemplified by interferon alfa 5 mRNA

2015
PMCID: 4565877
PMID: 25900662
DOI: 10.1007/s00018-015-1908-0

[…] The IPKnot program [] predicted a pseudoknot between contiguous sequences (G312CAG315) and (C317CUU320), pairing with (C420UGU423) and (A337AGG340), respectively. We focused on the first pair of annealing […]

library_books

Computational modeling of RNA 3D structures, with the aid of experimental restraints

2014
RNA Biol
PMCID: 4152360
PMID: 24785264
DOI: 10.4161/rna.28826

[…] any of the above-mentioned programs ignore such interactions for the sake of computational speed, there are algorithms that specialize in predictions for potentially pseudoknotted structures, such as IPknot.Our group has recently published a large-scale test of base-pairing prediction methods that compares their accuracy for different types of RNAs, when used with sequence information alone, i.e., […]

Citations

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IPknot institution(s)
Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba; Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara; Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto; Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan

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