Protocols

KnotSeeker specifications

Information


Unique identifier OMICS_09280
Name KnotSeeker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data RNA sequence
Operating system Unix/Linux
Programming languages C, C++, Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Jana Sperschneider

Information


Unique identifier OMICS_09280
Name KnotSeeker
Interface Web user interface
Restrictions to use None
Input data RNA sequence
Programming languages C, C++, Python
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jana Sperschneider

Publication for KnotSeeker

KnotSeeker citations

 (2)
call_split

The Putative Leishmania Telomerase RNA (LeishTER) Undergoes Trans Splicing and Contains a Conserved Template Sequence

2014
PLoS One
PMCID: 4229120
PMID: 25391020
DOI: 10.1371/journal.pone.0112061
call_split See protocol

[…] or all five Leishmania species analyzed, and then the constraints from the consensus structure were applied to the individual TER modeling by the execution of mfold with default parameters . Pknots , KnotSeeker , and Turbofold algorithms were applied without any success in our attempt to detect pseudoknots along the entire Leishmania TER sequences. […]

call_split

Evolutionary genomics of mycovirus related dsRNA viruses reveals cross family horizontal gene transfer and evolution of diverse viral lineages

2012
BMC Evol Biol
PMCID: 3483285
PMID: 22716092
DOI: 10.1186/1471-2148-12-91
call_split See protocol

[…] Searches for protein domains were performed using NCBI conserved domain database (CDD) (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi). The pseudoknot structure of L-dsRNA was predicted by the KnotSeeker program [] and was visualized using program VARNAv3-7 []. […]

KnotSeeker institution(s)
School of Computer Science and Software Engineering, University of Western Australia, Perth, WA, Australia; Institut für Informatik, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany

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