PseudoBase
Names
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PseudoBase
metasource: Fairsharing.org
version: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Pseudobase
metasource: re3data.org
version: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
A Pseudoknot Database
metasource: re3data.org
version: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
Names
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PseudoBase
metasource: Fairsharing.orgversion: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Pseudobase
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
A Pseudoknot Database
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
Other names: Pseudobase, A Pseudoknot Database
Names
More detailed information about this field from each metasource.
PseudoBase
metasource: Fairsharing.orgversion: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Pseudobase
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
A Pseudoknot Database
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
PseudoBase is a collection of RNA pseudoknots that have been made available for retrieval to the scientific community.
Description
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PseudoBase is a collection of RNA pseudoknots that have been made available for retrieval to the scientific community.
metasource: Fairsharing.orgversion: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Since the first discovery of RNA pseudoknots more and many more pseudoknots have been found. However, not all of those pseudoknot data are easy to trace. Sometimes the information is hidden in a publication where the title gives no hint that pseudoknot information is there. This was the first reason that we thought that a general accessible information source for pseudoknots would be handy.
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
Webpage:
http://www.ekevanbatenburg.nl/pbWebpage
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http://www.ekevanbatenburg.nl/pb
metasource: Fairsharing.orgversion: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://www.ekevanbatenburg.nl/PKBASE/PKB.HTML
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
Licence:
Name: otherLicence name
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other
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
Licence URL
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http://www.ekevanbatenburg.nl/PKBASE/PKBABOUT.HTML#s6
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
PseudoBase: a database with RNA pseudoknots
PMID: 10592225
metasource: Fairsharing.org
version: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
PseudoBase: structural information on RNA pseudoknots
PMID: 11125088
metasource: Fairsharing.org
version: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots
PMID: 18988624
metasource: Fairsharing.org
version: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Publications
More detailed information about this field from each metasource.
PseudoBase: a database with RNA pseudoknots
PMID: 10592225
metasource: Fairsharing.org
version: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
PseudoBase: structural information on RNA pseudoknots
PMID: 11125088
metasource: Fairsharing.org
version: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots
PMID: 18988624
metasource: Fairsharing.org
version: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
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PseudoBase: a database with RNA pseudoknots
PubMed citations: 47.
47 articles citing: PseudoBase: a database with RNA pseudoknots
Role of an RNA pseudoknot involving the polyA tail in replication of Pepino mosaic potexvirus and related plant viruses. PMID:35798958
RNA folding using quantum computers. PMID:35404931
Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution. PMID:34550747
A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots. PMID:31353036
bpRNA: large-scale automated annotation and analysis of RNA secondary structure. PMID:29746666
Synthesizing topological structures containing RNA. PMID:28361879
An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures. PMID:27499762
A Dynamic 3D Graphical Representation for RNA Structure Analysis and Its Application in Non-Coding RNA Classification. PMID:27213271
Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach. PMID:26478223
Multi-objective optimization for RNA design with multiple target secondary structures. PMID:26335276
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores. PMID:25727492
Characteristics and prediction of RNA structure. PMID:25110687
Tuning a riboswitch response through structural extension of a pseudoknot. PMID:23940363
Efficient known ncRNA search including pseudoknots. PMID:23369049
Predicting pseudoknotted structures across two RNA sequences. PMID:23044552
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. PMID:22600734
Multi-objective genetic algorithm for pseudoknotted RNA sequence design. PMID:22558001
Theory for RNA folding, stretching, and melting including loops and salt. PMID:21641320
RAG: an update to the RNA-As-Graphs resource. PMID:21627789
Sparsification of RNA structure prediction including pseudoknots. PMID:21194463
CyloFold: secondary structure prediction including pseudoknots. PMID:20501603
A comparative taxonomy of parallel algorithms for RNA secondary structure prediction. PMID:20458364
DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model. PMID:20123730
Fluorescence competition assay measurements of free energy changes for RNA pseudoknots. PMID:19921809
RNA folding on the 3D triangular lattice. PMID:19891777
RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology. PMID:19885376
Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints. PMID:19397915
Predicting structures and stabilities for H-type pseudoknots with interhelix loops. PMID:19237463
Prediction of RNA secondary structure with pseudoknots using integer programming. PMID:19208139
PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. PMID:18988624
Annotation of tertiary interactions in RNA structures reveals variations and correlations. PMID:18957492
Software.ncrna.org: web servers for analyses of RNA sequences. PMID:18440970
KnotSeeker: heuristic pseudoknot detection in long RNA sequences. PMID:18314500
Introduction to special issue on RNA. PMID:17938928
Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition. PMID:17906862
FSDB: a frameshift signal database. PMID:17631420
Predicting RNA secondary structures with pseudoknots by MCMC sampling. PMID:17589847
High sensitivity RNA pseudoknot prediction. PMID:17179177
Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. PMID:17069639
Predicting RNA pseudoknot folding thermodynamics. PMID:16709732
A heuristic approach for detecting RNA H-type pseudoknots. PMID:15994188
Asymmetry in RNA pseudoknots: observation and theory. PMID:15831794
Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs. PMID:15745998
Predicting genes expressed via -1 and +1 frameshifts. PMID:15371551
RAG: RNA-As-Graphs web resource. PMID:15238163
PseudoBase: structural information on RNA pseudoknots. PMID:11125088
Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. PMID:11095680 -
PseudoBase: structural information on RNA pseudoknots
PubMed citations: 31.
31 articles citing: PseudoBase: structural information on RNA pseudoknots
RNA folding using quantum computers. PMID:35404931
Review of machine learning methods for RNA secondary structure prediction. PMID:34437528
An RNA pseudoknot is essential for standby-mediated translation of the tisB toxin mRNA in Escherichia coli. PMID:33231643
An efficient simulated annealing algorithm for the RNA secondary structure prediction with Pseudoknots. PMID:31881969
A quantitative characterization of interaction between prion protein with nucleic acids. PMID:29872743
Structure and function of pseudoknots involved in gene expression control. PMID:25044223
A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures. PMID:24884954
Asymptotic structural properties of quasi-random saturated structures of RNA. PMID:24156624
A Tool Preference Choice Method for RNA Secondary Structure Prediction by SVM with Statistical Tests. PMID:23641141
Conformational features of topologically classified RNA secondary structures. PMID:22792195
On the page number of RNA secondary structures with pseudoknots. PMID:22159642
Understanding the transcriptome through RNA structure. PMID:21850044
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. PMID:21685106
Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins. PMID:21098139
ProbKnot: fast prediction of RNA secondary structure including pseudoknots. PMID:20699301
Thermodynamics of RNA structures by Wang-Landau sampling. PMID:20529917
CyloFold: secondary structure prediction including pseudoknots. PMID:20501603
Computing folding pathways between RNA secondary structures. PMID:20044352
Improved free energy parameters for RNA pseudoknotted secondary structure prediction. PMID:19933322
Rfam: updates to the RNA families database. PMID:18953034
KnotInFrame: prediction of -1 ribosomal frameshift events. PMID:18820303
RNA STRAND: the RNA secondary structure and statistical analysis database. PMID:18700982
The stimulatory RNA of the Visna-Maedi retrovirus ribosomal frameshifting signal is an unusual pseudoknot with an interstem element. PMID:18495941
Viral RNA pseudoknots: versatile motifs in gene expression and replication. PMID:17632571
PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures. PMID:16845039
HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. PMID:16199760
A heuristic approach for detecting RNA H-type pseudoknots. PMID:15994188
PSEUDOVIEWER2: Visualization of RNA pseudoknots of any type. PMID:12824341
Rfam: an RNA family database. PMID:12520045
Prediction of consensus structural motifs in a family of coregulated RNA sequences. PMID:12202774
Searching for RNA genes using base-composition statistics. PMID:11972348 -
PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots
PubMed citations: 22.
22 articles citing: PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots
RNA folding using quantum computers. PMID:35404931
Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution. PMID:34550747
High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove. PMID:31792448
A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots. PMID:31353036
An algebraic language for RNA pseudoknots comparison. PMID:30999864
Bi-objective integer programming for RNA secondary structure prediction with pseudoknots. PMID:29334887
RNA inverse folding using Monte Carlo tree search. PMID:29110632
URS DataBase: universe of RNA structures and their motifs. PMID:27242032
antaRNA--Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization. PMID:26581440
Pseudoknots in RNA folding landscapes. PMID:26428288
DSSR: an integrated software tool for dissecting the spatial structure of RNA. PMID:26184874
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores. PMID:25727492
Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce. PMID:24564983
Structural determinants for ligand capture by a class II preQ1 riboswitch. PMID:24469808
Algebraic and combinatorial properties of common RNA pseudoknot classes with applications. PMID:23057823
On the page number of RNA secondary structures with pseudoknots. PMID:22159642
The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral cap-independent translation element. PMID:21645857
RAG: an update to the RNA-As-Graphs resource. PMID:21627789
Computing the partition function for kinetically trapped RNA secondary structures. PMID:21297972
RNA pseudoknots: folding and finding. PMID:20495679
A comparative taxonomy of parallel algorithms for RNA secondary structure prediction. PMID:20458364
Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships. PMID:19369331
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Tags
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pathogen
metasource: Fairsharing.org
version: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
pseudoknot
metasource: Fairsharing.org
version: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
rna sequence
metasource: re3data.org
version: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
base sequence
metasource: re3data.org
version: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
dynamic programming algorithm
metasource: re3data.org
version: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
molecular biology
metasource: re3data.org
version: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
nucleis acid conformation
metasource: re3data.org
version: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
Tags
More detailed information about this field from each metasource.
pathogen
metasource: Fairsharing.orgversion: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
pseudoknot
metasource: Fairsharing.orgversion: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
ribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: PseudoBase; PseudoBase; DOI: https://doi.org/10.25504/FAIRsharing.5ey5w6; Last edited: April 26, 2021, 3:43 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
rna sequence
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
base sequence
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
dynamic programming algorithm
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
molecular biology
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
nucleis acid conformation
metasource: re3data.orgversion: re3data.org: Pseudobase; editing status 2017-05-23; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3D03N last accessed: 2022-11-04
pathogen pseudoknot rna rna sequence base sequence dynamic programming algorithm molecular biology nucleis acid conformation
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