Understanding the biological functions of an RNA molecule is tightly linked to the comprehension of its folding abilities. The folding process for an RNA molecule is achieved through the establishment of secondary and tertiary structures. Both states are interconnected and made with complex biological objects that need adapted visualization tools for their interactive exploration.
In this tutorial, Fabrice Jossinet will expose the basic principles of RNA architectures and illustrate them with Assemble2. You will also practice with Assemble2 in order to reveal the folding properties of your RNA molecule. Among the different features that are available with Assemble2, you will more precisely learn how to:
• Combine bioinformatics predictions and experimental data (structure probing, NGS reads,…) to quickly identify the best candidates for a secondary structure.
• Identify the consensus secondary structure for a set a related/orthologous RNA molecules.
• Annotate a solved tertiary structure into a secondary one that can be used as a 3D exploration guide.
• Edit an RNA secondary structure interactively to fit your experimental data and/or hypothesis.
• Derive a new tertiary structure from a solved one using an user-driven mutagenesis approach (deletion, insertion and/or substitution of single residues).
• Use an RNA secondary structure to query a database of recurrent RNA 3D motifs extracted from solved structures.
• Construct a 3D model from scratch for an entire RNA molecule or domain.
Tags: Assemble2, data visualization, RNA, RNA structure, tutorial, VIZBI, VIZBI 2014