ArticleNucleic acids research2010
DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- Possible involvement of three-stemmed pseudoknots in regulating translational initiation in human mRNAs.PloS one · 2024Article
- The virome of the invasive Asian bush mosquitoVirus evolution · 2023Article
- Linear-Time Algorithms for RNA Structure Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- Molecular Characterization of Novel Mycoviruses in SevenViruses · 2022Article
- The RNA pseudoknots in foot-and-mouth disease virus are dispensable for genome replication, but essential for the production of infectious virus.PLoS pathogens · 2022Article
- Molecular characterization of a novel victorivirus infecting Corynespora cassiicola.Archives of virology · 2022Article
- In silico analysis of local RNA secondary structure in influenza virus A, B and C finds evidence of widespread ordered stability but little evidence of significant covariation.Scientific reports · 2022Article
- Tolerance of Senecavirus A to Mutations in Its Kissing-Loop or Pseudoknot Structure Computationally Predicted in 3' Untranslated Region.Frontiers in microbiology · 2022Article
- The 5'-end motif of Senecavirus A cDNA clone is genetically modified in 36 different ways for uncovering profiles of virus recovery.Frontiers in microbiology · 2022Article
- Article
- Widespread ribosome stalling in a genome-reduced bacterium and the need for translational quality control.iScience · 2021Article
- Complete Genomic Characterization of Two Beet Soil-Borne Virus Isolates from Turkey: Implications of Comparative Analysis of Genome Sequences.The plant pathology journal · 2021Article
- IsRNA1:Journal of chemical theory and computation · 2021Article
- LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities.Bioinformatics (Oxford, England) · 2020Article
- A Novel RNA Virus Related to Sobemoviruses Confers Hypovirulence on the Phytopathogenic Fungus Sclerotinia sclerotiorum.Viruses · 2019Article
- Novel Victorivirus from a Pakistani Isolate ofViruses · 2019Article
- Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes.PloS one · 2019Article
- RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model.PloS one · 2018Article
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2 authors.
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Abstract
RNA pseudoknots are functional structure elements with key roles in viral and cellular processes. Prediction of a pseudoknotted minimum free energy structure is an NP-complete problem. Practical algorithms for RNA structure prediction including restricted classes of pseudoknots suffer from high runtime and poor accuracy for longer sequences. A heuristic approach is to search for promising pseudoknot candidates in a sequence and verify those. Afterwards, the detected pseudoknots can be further analysed using bioinformatics or laboratory techniques. We present a novel pseudoknot detection method called DotKnot that extracts stem regions from the secondary structure probability dot plot and assembles pseudoknot candidates in a constructive fashion. We evaluate pseudoknot free energies using novel parameters, which have recently become available. We show that the conventional probability dot plot makes a wide class of pseudoknots including those with bulged stems manageable in an explicit fashion. The energy parameters now become the limiting factor in pseudoknot prediction. DotKnot is an efficient method for long sequences, which finds pseudoknots with higher accuracy compared to other known prediction algorithms. DotKnot is accessible as a web server at http://dotknot.csse.uwa.edu.au.
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