ArticleBioinformatics (Oxford, England)2012
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Using the RNAstructure Software Package to Predict Conserved RNA Structures.Current protocols · 2024Article
- How to benchmark RNA secondary structure prediction accuracy.Methods (San Diego, Calif.) · 2019Review
- Prediction of the secondary structure of short DNA aptamers.Biophysics and physicobiology · 2019Article
- Accelerated RNA secondary structure design using preselected sequences for helices and loops.RNA (New York, N.Y.) · 2018Article
- TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.Nucleic acids research · 2017Article
- Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.PLoS computational biology · 2017Article
- Bridging the gap between in vitro and in vivo RNA folding.Quarterly reviews of biophysics · 2016Article
- URS DataBase: universe of RNA structures and their motifs.Database : the journal of biological databases and curation · 2016Article
- Dynalign II: common secondary structure prediction for RNA homologs with domain insertions.Nucleic acids research · 2014Article
- The centrality of RNA for engineering gene expression.Biotechnology journal · 2013Review
- Accelerating calculations of RNA secondary structure partition functions using GPUs.Algorithms for molecular biology : AMB · 2013Article
- RNAstructure: Web servers for RNA secondary structure prediction and analysis.Nucleic acids research · 2013Article
- Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM.BMC bioinformatics · 2013Article
- Computational analysis of noncoding RNAs.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
2 authors.
Funding
Abstract
motivationMany 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.
resultsTurboKnot 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.
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Registered trials
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