General Information
| Description | Rapid prediction of conserved RNA secondary structures including pseudoknots |
| Homepage | http://rna.urmc.rochester.edu |
Publications
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots
Motivation:
Many RNA molecules function without being translated into proteins, and function depends on structure. Pseudoknots are motifs in RNA secondary structures that are difficult to predict but are also often functionally important.
Results:
TurboKnot is a new algorithm for predicting the secondary structure, including pseudoknotted pairs, conserved across multiple sequences. TurboKnot finds 81.6% of all known base pairs in the systems tested, and 75.6% of predicted pairs were found in the known structures. Pseudoknots are found with half or better of the false-positive rate of previous methods.
Availability:
The program is available for download under an open-source license as part of the RNAstructure package at: http://rna.urmc.rochester.edu.
Contact:
david_mathews@urmc.rochester.edu
Supplementary information:
Supplementary data are available at Bioinformatics online.
Related Tools
IPknot
Published June 2011
Fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
DAFS
Published October 2012
Simultaneous aligning and folding of RNA sequences via dual decomposition
StatAlign 2.0
Published January 2013
Combining statistical alignment with RNA secondary structure prediction
Forna (force-directed RNA)
Published June 2015
Simple and effective online RNA secondary structure diagrams
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