RNA Folding Prediction Quiz

The 'amount of information (bits)' obtained about one variable via observing the other variable.

States M (including match states, insert states, and delete states), and symbol emission probabilities.

To develop covariance models (CMs) that can be applied to search genomes for RNA elements based on recognizing RNA folds.

<p>It is a measure of 'linear dependence' between the two random variables.</p> Signup and view all the answers

<p>To predict RNA families based on input sequences in fasta format.</p> Signup and view all the answers

<p>It provides best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.</p> Signup and view all the answers

<p>To provide comparative analysis of RNA sequences.</p> Signup and view all the answers

<p>To identify riboswitch RNAs.</p> Signup and view all the answers

<p>It is used for the analysis of regulatory RNA elements.</p> Signup and view all the answers

<p>It uses convolutional deep learning neural networks for prediction of prokaryotic and eukaryotic promoters.</p> Signup and view all the answers

<p>It is a simple prediction tool for prokaryote promoters.</p> Signup and view all the answers

<p>It is a neural network-based classifier for σ70 promoter prediction in Pseudomonas.</p> Signup and view all the answers

<p>Some examples of regulatory significance of RNA folding include transcriptional and translational stops, speed of translation and folding of peptides stabilizing rRNA 2nd and 3D structures, riboswitches involving metabolites, RNA foldback (translation), RNAi and miRNAs, siRNAs, RNA thermometers (i.e. heat shock) attenuation, and ribozymes.</p> Signup and view all the answers

<p>RNA is considered the foundation supporting the DNA world because it has regulatory significance in various cellular processes, including transcriptional and translational stops, RNA foldback, riboswitches, and ribozymes. Additionally, RNA serves as the template for protein synthesis through mRNAs and as a constituent of ribosomes.</p> Signup and view all the answers

<p>The classic RNAs mediating protein synthesis and regulatory RNAs include mRNAs (messenger RNAs) and rRNAs (ribosomal RNAs). mRNAs act as templates for protein synthesis, while rRNAs are RNA constituents of ribosomes, which decode mRNAs into amino acid sequences of proteins.</p> Signup and view all the answers

<p>Some examples of small non-coding RNAs include miRNA, siRNA, and piRNA. These RNAs are involved in regulatory processes and are not solely dedicated to the translation of proteins.</p> Signup and view all the answers

<p>H-bonding, Van der Waals interactions, and hydrophobic interactions</p> Signup and view all the answers

<p>Long-range interactions may be missed by the program if not specified by the user.</p> Signup and view all the answers

<p>Pseudoknots cannot be predicted with Mfold, and they hold diverse functions in RNA structures.</p> Signup and view all the answers

<p>Integration of tools is necessary for studying the evolution of ITS regions within a group of organisms, and Mfold can be used to understand the function of ITS regions and assess their utility for molecular taxonomy.</p> Signup and view all the answers

<p>H-bonding, Van der Waals interactions, and hydrophobic interactions</p> Signup and view all the answers

<p>The UNAFold web server is part of the 'Unafold' and offers a new and improved interface for Mfold.</p> Signup and view all the answers

<p>The web server also provides the option to force a string of consecutive base pairs and apply constraints based on comparative analysis with other structures.</p> Signup and view all the answers

<p>Recent applications of sequence logos show conservation of positions due to structural constraints, requiring the coding of structural elements into the Vienna notation.</p> Signup and view all the answers

<p>Mfold is a web server for nucleic acid folding and hybridization prediction, using nearest neighbor thermodynamic rules.</p> Signup and view all the answers

<p>Different environmental conditions can be modified in the advanced version of Mfold.</p> Signup and view all the answers

<p>It provides mathematically predicted structures, but these may not be the actual biological structures.</p> Signup and view all the answers

<p>Pseudoknots cannot be predicted with Mfold, and they hold diverse functions in RNA structures.</p> Signup and view all the answers

<p>tRNAs are adapter molecules that carry individual amino acids to the site of protein synthesis and recognize specific codons in mRNA.</p> Signup and view all the answers

<p>snoRNAs modify ribosomal RNAs, while snRNAs are involved in splicing spliceosomal introns.</p> Signup and view all the answers

<p>siRNAs are small RNAs formed through cleavage of long double-stranded RNA molecules and are important for taming the activity of transposons and combating viral infection.</p> Signup and view all the answers

<p>miRNAs are small RNAs encoded by specific genes and function in repressing mRNA translation or degradation in plants and animals.</p> Signup and view all the answers

<p>piRNAs are small RNAs essential for the development of germ cells and function in silencing repetitive regions and transposons.</p> Signup and view all the answers

<p>Long non-coding RNAs (lncRNAs) participate in various cellular processes, including mRNA splicing and ribosome biogenesis.</p> Signup and view all the answers

<p>circRNAs can encode proteins and have regulatory functions, often being biproducts of intron splicing.</p> Signup and view all the answers

<p>RNA folding can impact the rate of translation and influence the folding of the peptide during translation, and RNA folds can be targets for viral nucleases or other proteins.</p> Signup and view all the answers

<p>Certain RNA molecules, such as ribozymes, have conserved RNA folds, and group I and group II introns have specific secondary structures with unique features.</p> Signup and view all the answers

<p>RNA folding tools like ViennaRNA, RNAweasel, and Sfold are used to predict RNA structures and features, with the need for manual adjustments and new generation programs that incorporate comparative analysis.</p> Signup and view all the answers

<p>Vienna notation is used for RNA folding predictions, with symbols indicating base pairings, loops, and segments that are variable.</p> Signup and view all the answers