Accurate SHAPE-directed RNA structure determination
نویسندگان
چکیده
منابع مشابه
Accurate 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 کاملAccurate 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 کاملSHAPE directed RNA folding
SUMMARY Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics-based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary struc...
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 کاملEvaluating the accuracy of SHAPE-directed RNA secondary structure predictions
Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set of 16S/18S ribosomal sequences using a stochastic model of experimental SHAPE data. The average accuracy for 1000 data-directed predictions always ...
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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 2008
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.0806929106