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 repertoire 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.


Recent Changes

Summary of changes as of May 5th, 2018:

Summary of changes as of June 24th, 2015:

  • Expanding the tree database to include structures with up to 13 vertices (approx. 260 nucleotides)
  • Evaluate and catalog newly found RNAs since the last update of 2011 and include chain information
  • Use of k2n to convert knotted structures to pseudoknot-free RNAs

Summary of changes as of March 24th, 2011:

  • Discovery of 37 newly-confirmed tree graph and 44 newly-confirmed dual graph topologies
  • Reclassification of candidate topologies using k-NN clustering with training data from existing RNAs
  • Addition of example RNA secondary structures from the RNA Strand, PseudoBase++, and Rfam Databases to each topology's sub-page
  • Dual graph functionality added to RNAMatrix
  • Removal of the limitations of 10 vertices and 200 nucleotides from RNAMatrix for tree graphs
  • Enhanced search features
  • Redesign of topology pages and database; each topology's sub-page is linked via PHP to the core database


(Access to Original RAG2D 2004)

Page | by Dr. Radut