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)The Putative Leishmania Telomerase RNA (LeishTER) Undergoes Trans Splicing and Contains a Conserved Template Sequence
[…] 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. […]
Evolutionary genomics of mycovirus related dsRNA viruses reveals cross family horizontal gene transfer and evolution of diverse viral lineages
[…] 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 []. […]
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