ProbKnot: Fast prediction of RNA secondary structure including pseudoknots
نویسندگان
چکیده
منابع مشابه
CyloFold: secondary structure prediction including pseudoknots
UNLABELLED Computational RNA secondary structure prediction approaches differ by the way RNA pseudoknot interactions are handled. For reasons of computational efficiency, most approaches only allow a limited class of pseudoknot interactions or are not considering them at all. Here we present a computational method for RNA secondary structure prediction that is not restricted in terms of pseudok...
متن کاملRNA Secondary Structure Prediction with Simple Pseudoknots
Pseudoknots are widely occurring structural motifs in RNA. Pseudoknots have been shown to be functionally important in different RNAs which play regulatory, catalytic, or structural roles in cells. Current biophysical methods to identify the presence of pseudoknots are extremely time consuming and expensive. Therefore, bioinformatics approaches to accurately predict such structures are highly d...
متن کاملHotKnots: heuristic prediction of RNA secondary structures including pseudoknots.
We present HotKnots, a new heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, our algorithm explores many alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate stems. In an empirical evaluation of the...
متن کاملTurboKnot: 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 fi...
متن کاملNew Heuristic Algorithm of RNA Structure Prediction Including Pseudoknots
Computational models and methods for predicting secondary structure of RNA sequence are in demand. Based on MFE principle and the relative stability of the n-stems in RNA molecules, Minimum Free Energy method is adopted widely to predict RNA secondary structure. An improved heuristic algorithm is presented to predict RNA pseudoknotted structure, and it can compute arbitrary pseudoknots. The alg...
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ژورنال
عنوان ژورنال: RNA
سال: 2010
ISSN: 1355-8382
DOI: 10.1261/rna.2125310