ProbKnot: Fast prediction of RNA secondary structure including pseudoknots
- 10 August 2010
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in RNA
- Vol. 16 (10) , 1870-1880
- https://doi.org/10.1261/rna.2125310
Abstract
It is a significant challenge to predict RNA secondary structures including pseudoknots. Here, a new algorithm capable of predicting pseudoknots of any topology, ProbKnot, is reported. ProbKnot assembles maximum expected accuracy structures from computed base-pairing probabilities in O(N2) time, where N is the length of the sequence. The performance of ProbKnot was measured by comparing predicted structures with known structures for a large database of RNA sequences with fewer than 700 nucleotides. The percentage of known pairs correctly predicted was 69.3%. Additionally, the percentage of predicted pairs in the known structure was 61.3%. This performance is the highest of four tested algorithms that are capable of pseudoknot prediction. The program is available for download at: http://rna.urmc.rochester.edu/RNAstructure.html.Keywords
This publication has 71 references indexed in Scilit:
- RNAstructure: software for RNA secondary structure prediction and analysisBMC Bioinformatics, 2010
- Prediction of RNA secondary structure with pseudoknots using integer programmingBMC Bioinformatics, 2009
- Rfam: updates to the RNA families databaseNucleic Acids Research, 2008
- The RNA WikiProject: Community annotation of RNA familiesRNA, 2008
- The Vienna RNA WebsuiteNucleic Acids Research, 2008
- Let Me Count the Ways: Mechanisms of Gene Regulation by miRNAs and siRNAsMolecular Cell, 2008
- Predicting RNA pseudoknot folding thermodynamicsNucleic Acids Research, 2006
- Non–coding RNA genes and the modern RNA worldNature Reviews Genetics, 2001
- Thermodynamics of Three-Way Multibranch Loops in RNABiochemistry, 2001
- The Structural Basis of Ribosome Activity in Peptide Bond SynthesisScience, 2000