Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
نویسندگان
چکیده
منابع مشابه
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.
A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, thes...
متن کاملStatistical analysis of SHAPE-directed RNA secondary structure modeling.
The ability to predict RNA secondary structure is fundamental for understanding and manipulating RNA function. The information obtained from selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments greatly improves the accuracy of RNA secondary structure prediction. Recently, Das and colleagues [Kladwang, W., et al. (2011) Biochemistry 50, 8049-8056] proposed a "bootstra...
متن کاملPredicting RNA Secondary Structures Including Pseudoknots
RNA secondary structures play a vital role in modern genetics and a lot of time and e ort has been put into their study. It is important to be able to predict them with high accuracy, since methods involving manual analysis are expensive, time-consuming and error-prone. Predictions can also be used to guide experiments to reduce time and money requirements. Several algorithms have been develope...
متن کاملAccurate SHAPE-directed RNA structure determination.
Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure-function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a s...
متن کاملCyloFold: 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...
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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 2013
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.1219988110