RNA Folding Prediction Quiz

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Questions and Answers

What does Mutual Information (MI) theory aim to quantify?

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

What does the Covariance Model (CM) describe?

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

What is the purpose of Structural Alignment and Covariation Analysis of RNA Sequences?

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

What is the purpose of the INFERNAL covariance?

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

What is the purpose of StructRNAfinder?

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

What is the RNA workbench used for?

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

What is the purpose of the TurboFold Web Server Comparative Analysis?

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

What is the purpose of the Riboswitch finder tool?

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

What is the function of the CMBL-PATLOC Pattern Locator?

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

What is the approach implemented in the SoftBerry - cnnpromoter program?

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

What is the purpose of Genome2D?

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

What is the function of the Bacterial SAPPHIRE Sequence Analyser?

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

What are some examples of regulatory significance of RNA folding?

<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

What is the role of RNA in the foundation supporting the DNA world?

<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

What are the classic RNAs mediating protein synthesis and regulatory RNAs?

<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

What are some examples of small non-coding RNAs?

<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

  1. What kind of interactions does Mfold consider for RNA and DNA secondary structure prediction?

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

  1. What is one limitation of Mfold in predicting RNA and DNA structures?

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

  1. Why can't pseudoknots be predicted with Mfold?

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

  1. What is the purpose of integrating tools when studying the evolution of ITS regions within a group of organisms?

<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

  1. What kind of interactions does Mfold consider for RNA and DNA secondary structure prediction?

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

  1. What is the role of the UNAFold web server in relation to Mfold?

<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

  1. What additional options does the Mfold web server provide for studying RNA structures?

<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

  1. What is the recent application of sequence logos in relation to Mfold?

<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

  1. How does Mfold handle the prediction of nucleic acid folding and hybridization?

<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

  1. What modification can be made in the advanced version of Mfold?

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

  1. What may not be the actual biological structures provided by Mfold?

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

  1. What cannot be predicted with Mfold and what is their significance in RNA structures?

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

  1. What is the function of tRNAs in the process of protein synthesis and mRNA recognition?

<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

  1. What are the roles of snoRNAs and snRNAs in RNA modification and splicing?

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

  1. How are siRNAs formed and what are their roles in regulating transposon activity and viral infection?

<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

  1. What is the function of miRNAs and how are they encoded?

<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

  1. What are piRNAs and what is their essential role in cellular development and gene silencing?

<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

  1. In what cellular processes do long non-coding RNAs (lncRNAs) participate, and what are their functions?

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

  1. What are the characteristics and functions of circRNAs?

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

  1. What are the different types of regulatory RNA molecules mentioned in the text, and how are they derived?

<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

  1. What are some examples of conserved RNA folds and specific secondary structures mentioned in the text?

<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

  1. What are some tools used for predicting RNA structures, and what adjustments and advancements are mentioned in the text?

<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

  1. What notation is used for RNA folding predictions, and what do the symbols indicate?

<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

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Study Notes

Functions and Types of Regulatory RNA Molecules

  • tRNAs are adapter molecules that carry individual amino acids to the site of protein synthesis and recognize specific codons in mRNA.
  • snoRNAs modify ribosomal RNAs, while snRNAs are involved in splicing spliceosomal introns.
  • 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.
  • miRNAs are small RNAs encoded by specific genes and function in repressing mRNA translation or degradation in plants and animals.
  • piRNAs are small RNAs essential for the development of germ cells and function in silencing repetitive regions and transposons.
  • Long non-coding RNAs (lncRNAs) participate in various cellular processes, including mRNA splicing and ribosome biogenesis.
  • circRNAs can encode proteins and have regulatory functions, often being biproducts of intron splicing.
  • Regulatory RNA, including small noncoding RNAs, has various types such as siRNA, miRNA, and piRNA, each derived from specific RNA molecules.
  • 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.
  • Certain RNA molecules, such as ribozymes, have conserved RNA folds, and group I and group II introns have specific secondary structures with unique features.
  • 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.
  • Vienna notation is used for RNA folding predictions, with symbols indicating base pairings, loops, and segments that are variable.

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