Funded by the NSF and NIH


Our RAG Database aims to classify and analyze existing RNAs according to their topological characteristics in the goal of exploring RNA's reportoire and thus contributing to RNA design and structure prediction. Our analysis is based on the description of RNAs as graphs, that is, using network theory to describe RNA secondary structures.  We represent RNA topologies as planar tree graphs or dual graphs. Essentially, RNA graphs specify the connectivity between RNA secondary structural elements (i.e., loops, bulges, junctions, and stems). Graphical representation of RNA structures allows us to explore the 'RNA space' and analyze structural/functional relationships between RNAs using methods in graph theory.


Use the RNA tutorial section to learn about useful topics that will help you navigate through the RAG Database. The tutorial topics include brief explanations of RNA Structure, Graph Theory and RNA Structures, Spectral Graph Analysis, Graph Isomorphism and Clustering RNA Motifs.

Tree Graphs

The Tree Graph Subproject uses graph theory to represent the possible structures of secondary RNA molecules. It contains a Subproject Description, a tutorial on How to produce RNA Tree Graphs, and a Database of RNA Tree Graphs

Dual Graphs

The Dual Graph Subproject provides a way to graphically represent tree, pseudoknot, and other RNA motifs. It contains a Subproject Description, a tutorial on  How to Represent All Types of RNA Motifs as Dual Graphs, and a Database of RNA Motifs


This RNA Matrix Computer Program converts an RNA secondary structure into a matrix representation of the RNA's graph. Specifically, it allows the "ct file" produced using Zuker's mFold to be uploaded in order to determine the number of vertices within the RNA structure as well as the Laplacian matrix and its associated eigenvalues. To learn more about the concepts that are involved with this program, please visit the Program Description

Useful Links

Links that might be useful in the navigation of this website as well as in the understanding of RNA structures include the Nucleic Acid Database, mFold, the Pseudobase, The RNA World Website at IMB-Jena, The 5S Ribosomal RNA Database and others.

RNA Glossary

This Glossary will help clarify the meanings of certain terms you will find throughout our database.


1.  Kim N, Shiffeldrim N, Gan HH, Schlick T. Candidates for novel RNA topologies ; J. Mol. Biol. 2004, 341(5):1129-44

2.  Zorn J, Gan HH, Shiffeldrim N, Schlick T. Structural motifs in ribosomal RNAs: implications for RNA design and genomics. ;Biopolymers. 2004, 73(3):340-7.

3.  Hin Hark Gan, Daniela Fera, Julie Zorn, Nahum Shiffeldrim, Michael Tang, Uri Laserson, Namhee Kim, and Tamar Schlick.  RAG: RNA-As-Graphs Database - Concepts, Analysis, and Features, Bioinformatics 2004, 20(8):1285-91 

4.  Hin Hark Gan, Samuela Pasquali, and Tamar Schlick. (2003) Exploring the repertoire of RNA secondary motifs using graph theory with implications for RNA design . Nucleic Acids Res., 31, 2926-2943. 

Please email T. Schlick at for further information.


RNA Team: Tamar Schlick (PI), Hin Hark Gan, Namhee Kim, Shereef Elmetwaly, Yurong xin, Giulio Quarta, Jin Sup Shin, Christian Laing


The project is supported by the National Science Foundation (NSF) and National Institutes of Health (NIH).

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Last Updated: July 10, 2007