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


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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 in publications

 (7)
library_books

Abstracts

PMCID: 5418514
DOI: 10.1111/jdi.12670

[…] impaired glucose tolerance on 75 gogtt at the age of 19. we found 6 nucleotides (ggggtt) insertion mutation in the 5′utr of hnf1a. centridfold predicted it may form a new stem‐loop structure and ipknot revealed that this structural change may affect the translational efficiency and decrease protein expression of hnf1a. we observed a significant reduction in expression of the mutant allele […]

PMCID: 5454406
PMID: 28445416
DOI: 10.3390/v9050093

[…] 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, […]

PMCID: 4748022
PMID: 26912953
DOI: 10.6026/97320630011512

[…] 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., this database contains three major utilities: (1) […]

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

[…] to destabilisation of the domains coaxial stacking and/or sterical facilitation of nucleases access to the central helix junction, greatly supported the proposed four-way junction structure., the ipknot program [] predicted a pseudoknot between contiguous sequences (g312cag315) and (c317cuu320), pairing with (c420ugu423) and (a337agg340), respectively. we focused on the first pair […]

PMCID: 4152360
PMID: 24785264
DOI: 10.4161/rna.28826

[…] 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, […]


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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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