(Georgia Institute of Technology, 2022-05)
McCann, Holly
Non-coding RNAs play key roles in cellular systems such as transcription and translation. Computational predictive methods provide insight into the secondary structures of non-coding RNAs from diverse organisms for which there are no high-quality crystal structures. This research project builds upon the existing framework of the R2DT (RNA 2D Templates) tool developed by the RNAcentral consortium with collaboration from Georgia Tech researchers. R2DT predicts RNA secondary structures and displays them in the form of a 2D topology diagram by using known, related structures as templates for prediction and visualization. The automated template-based approach, however, often ignores unique species-specific regions such as ribosomal RNA expansion segments.
To improve the functionality of R2DT, the secondary structures of insertion regions which are not found in any template structure are now predicted using the RNAfold algorithm developed by ViennaRNA. This hybrid approach can generate more accurate structures for various types of RNA molecules with unique features across entire phylogeny. In addition to improvements to the folding algorithm, a new front-end for R2DT has also been developed which builds on the PDBe RNA Viewer. The generated topology diagrams now display RNA secondary structures represented either as a contour line or as individual nucleotides. The improved RNA Viewer provides support for visualization of both canonical and non-canonical base pairs (using the symbolism proposed by Leontis and Westhof), and includes interactive features such as object highlighting and a tooltip. These developments improve the accuracy and functionality of computationally predicted RNA topology diagrams. The applet further enables users to visualize various structural and evolutionary data and to easily generate publication-quality images of data mapped onto secondary structures. This applet has been integrated with the PDB MSA and Mol* viewers to display non-coding RNA molecules and associated data in three dimensions on the RiboVision2 webserver.
(Georgia Institute of Technology, 2020-08)
Meade, Caeden Daniel
RiboVision is a collection of applications housed on servers at the Georgia Institute of Technology which serves to facilitate the development of publication-quality diagrams of ribosomal RNA (rRNA) and ribosomal protein (rProtein) structures (Petrov et. al, 2014). In particular, RiboVision seeks to promote analysis of key properties of rRNA and rProteins in primary, secondary, and tertiary structures.
As key semantides (ubiquitous macromolecules which carry genetic equivalent to the information intrinsic to DNA molecules and may be used by comparison to inform phylogenetic relationships), comparison of the primary and secondary structures of 16S and 18S RNA allows for the phylogenetic comparison of prokaryotic species and eukaryotic species, respectively (Fuerst, 2001). Sequence alignments are housed on the RiboVision server and stored in a MySQL database. Over the next two semesters, major improvements will be made to the server resulting in the newest edition, RiboVision3, which will feature improvements over the preceding RiboVision2 including the integration of XRNA, a program responsible for the generation of rRNA secondary structures and their exportation of their data into common computer-file formats (CSV, SVG, PDF, etc.) and the PDB Topology Viewer, a program responsible for production of protein secondary structures and their exportation into SVG image files.
The core functionality of XRNA - demonstration and editing tools of rRNA secondary structures needs to be iterated upon to allow for a more diverse set of purposes, including processing of high-quality hand-edited images into formats which are compatible with on-server management and conversion into formats native to web browsers.