Dual Graph Subproject Description
Home RNA
Dual Graph Subproject Home How
to Represent All Types of RNA Motifs as Dual Graphs
Database of RNA Dual Graphs

Background
Ribonucleic acid (RNA) molecules are important in the performance of biological processes in the cell. Some of their known roles include protein synthesis and transport, catalysis, and chromosome replication and regulation. Studies have shown that there are different types of RNA that perform the different biological functions. These RNA molecules have a vast number of structures. Using graph theory, we aim to describe and analyze these structures and apply the fingings to many important problems such as RNA design. Our graphical representations are limited to RNA secondary elements. Still, graph representation allows enumeration of RNA's repertoire. Since we find that only few RNAs have been found compared to the number of possible topologies, these graphs will help the search of missing RNA structures and stimulate the production of RNAs in the laboratory.
RNA trees and pseudoknots are two major types
of 2D RNA secondary structures, distinguished by the topology of their
base pairing patterns. An RNA tree is a branching network of helical stems
interrupted by bulges and junctions that end in loops, except at the 3'
and 5' ends. An RNA pseudoknot has a stretch of nucleotides within a hairpin
loop that pairs with nucleotides external to that loop. RNA trees
can be represented using tree graphs (see How to Produce RNA Tree Graphs).
However, tree graphs cannot represent RNA pseudoknot topologies. Moreover,
there is another RNA topological type which cannot be represented as trees:
RNAs with stems connected by a single strand. We call such structures RNA
bridges. Thus, more general (nontree) graphs are required to graphically
represent existing RNA trees, pseudoknots and bridges.
Purpose
To represent, catalogue and analyze existing and
hypothetical RNA trees, pseudoknots
and bridges.
Process
We begin this subproject by taking the pseudoknot
sequences available in Pseudobase
and drawing the corresponding pseudoknot structures which are then converted
into the dual graphs of this website's database. These dual graphs
provide a simplified image of what the actual secondary structures look
like, but they are more complex than the graphs provided in the Tree Graph
Database. Because of the simplicity of tree and dual graphs, we are
able to apply the tools of graph theory to study these graphs in more depth.
By using computational methods we calculate the corresponding Laplacian
matrices and their eigenvalues
for each graph. This allows us to analyze the various eigenvalues
and to search for clusters and relationships between the eigenvalues of
an RNA found in Nature and those for the RNA that have not yet been found.
Finally, these data and information will be applied to the design of RNA
as well as to the search of RNA.
Database Description
The dual graphs for the existing and nonexisting
RNAs are distinguished by color. In addition, we organize dual
graphs according to two different methods. In one approach, graphs
are ordered by the number of vertices. In the other method, graphs
are ordered by functional types or families. You may look at all
of the graphs with a particular number of vertices or of certain type at
any one time. In each grouping, graphs are ordered by the second
eigenvalue of their corresponding Laplacian matrix. More information
about a particular structure may be obtained by clicking on the graph.
Links to different parts of the rest of this database have been provided
as well as links to other useful databases and programs.