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DotKnot specifications

Information


Unique identifier OMICS_09283
Name DotKnot
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data RNA sequence
Input format Raw
Operating system Unix/Linux
Computer skills Advanced
Version 1.3.1
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Jana Sperschneider

Information


Unique identifier OMICS_09283
Name DotKnot
Interface Web user interface
Restrictions to use None
Input data RNA sequence
Input format Raw
Computer skills Basic
Version 1.3.1
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Jana Sperschneider

Publication for DotKnot

DotKnot citations

 (7)
library_books

New insights into the transposition mechanisms of IS6110 and its dynamic distribution between Mycobacterium tuberculosis Complex lineages

2018
PLoS Genet
PMCID: 5896891
PMID: 29649213
DOI: 10.1371/journal.pgen.1007282

[…] were predicted using the rna fold webserver (http://rna.tbi.univie.ac.at/cgi-bin/rnawebsuite/rnafold.cgi). pseudoknot structures and their estimated free energy were located and computed using dotknot (http://dotknot.csse.uwa.edu.au/)., mycobacterial cultures were grown to exponential phase (od600 = 0.5–0.6) and pelleted by centrifugation. to minimize rna degradation bacteria […]

library_books

Molecular Characterization of Novel Totivirus Like Double Stranded RNAs from Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust

2017
Front Microbiol
PMCID: 5641321
PMID: 29067018
DOI: 10.3389/fmicb.2017.01960

[…] center for biotechnology information (ncbi) orf finder program. motif searches were performed in three databases, including prosite, pfam and cdd. rna pseudoknot structure was predicted using the dotknot program and drawn with pseudoviewer3 (; )., phylogenetic trees were constructed based on the deduced amino acid sequences of the putative rdrp and cp regions using the maximum-likelihood (ml) […]

library_books

Multiple viral infections in Agaricus bisporus Characterisation of 18 unique RNA viruses and 8 ORFans identified by deep sequencing

2017
Sci Rep
PMCID: 5446422
PMID: 28550284
DOI: 10.1038/s41598-017-01592-9

[…] the maximum number of motifs to return was set to 20 and “search given strand only” was checked. other settings were kept as default. pseudoknots were predicted in both 5′utr and 3′ utr using dotknot_1.3.1., to confirm the correct assembly of each contig, pcr primer pairs were designed to generate overlapping products of 600–900 bp in length designed to cover the entire length […]

library_books

Topological constraints of structural elements in regulation of catalytic activity in HDV like self cleaving ribozymes

2016
Sci Rep
PMCID: 4908430
PMID: 27302490
DOI: 10.1038/srep28179

[…] experiment), ph 7.5, and either 0.3 or 1 mm mg2+., the activation energy, ea, is defined as, , the mfe for each form of ribozyme studied was determined by computational calculation using the dotknot software (available at http://dotknot.csse.uwa.edu.au/) using predictions for local psuedoknots and kissing hairpins. the full sequence of the transcribed ribozyme was input and used […]

library_books

The dsRNA Virus Papaya Meleira Virus and an ssRNA Virus Are Associated with Papaya Sticky Disease

2016
PLoS One
PMCID: 4863961
PMID: 27166626
DOI: 10.1371/journal.pone.0155240

[…] pmev and 4.5 kb for the second virus (pmev2) were scanned for the presence of orfs using genemark (http://exon.gatech.edu/genemark/eukhmm.cgi). prediction of pseudoknot structures was performed with dotknot [] using as input the 100-nt sequence immediately downstream of the putative heptanucleotide at the orf1-orf2 junction of the pmev coding strand., sequence identity/similarity for each orf […]

library_books

Identification of conserved RNA secondary structures at influenza B and C splice sites reveals similarities and differences between influenza A, B, and C

2014
BMC Res Notes
PMCID: 3895672
PMID: 24405943
DOI: 10.1186/1756-0500-7-22

[…] base pairing interactions in predicted loop regions. mc-fold utilizes high resolution rna structural information from the protein data bank (pdb) to estimate non-canonical base pairing energies., dotknot [], which folds single sequences, was used to predict pseudoknots in sequences containing splice sites. dotknot extracts possible stem regions from rna secondary structure partition function […]


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DotKnot institution(s)
School of Computer Science and Software Engineering, The University of Western Australia, Perth, WA, Australia

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