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Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
The ViennaRNA Package is software, a set of standalone programs and libraries used for predicting and analysing RNA nucleic acid secondary structures. [1] The source code for the package is released as free and open-source software and compiled binaries are available for the operating systems Linux, macOS, and Windows.
Sfold is a software program developed to predict probable RNA secondary structures through structure ensemble sampling and centroid predictions [1] [2] with a focus on assessment of RNA target accessibility, [3] for major applications to the rational design of siRNAs [4] in the suppression of gene expressions, and to the identification of targets for regulatory RNAs particularly microRNAs.
It has been suggested that signals other than those directly detectable in sequences may improve gene prediction. For example, the role of secondary structure in the identification of regulatory motifs has been reported. [13] In addition, it has been suggested that RNA secondary structure prediction helps splice site prediction. [14] [15] [16] [17]
Other methods, such as stochastic context-free grammars can also be used to predict nucleic acid secondary structure. For many RNA molecules, the secondary structure is highly important to the correct function of the RNA — often more so than the actual sequence. This fact aids in the analysis of non-coding RNA sometimes termed "RNA genes".
psRobot is a web-based tool for plant small RNA meta-analysis. psRobot computes stem-loop small RNA prediction, which aligns user uploaded sequences to the selected genome, extracts their predicted precursors, and predicts whether the precursors can fold into stem-loop shaped secondary structure. psRobot also computes small RNA target ...
RNA secondary structure is usually represented by the dot-bracket notation, with pairing round brackets indicating basepairs in a stem and dots representing loops. The interrupted stems of pseudoknots mean that such notation must be extended with extra brackets, or even letters, so that different sets of stems can be represented.
The scanning mechanism of Initiation starts when the PIC binds the 5′ end of the mRNA. Scanning is stimulated by Dhx29 and Ddx3/Ded1 and eIF4 proteins. [1] The Dhx29 and Ddx3/Ded1 are DEAD-box helicases that help to unwind any secondary mRNA structure which could hinder scanning. [17]
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