Searching through RNA database using subgraph isomorphism algorithm. This may take up to 20 minutes for complex structures.
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Graph-Based Structure Search
Draw your custom RNA motif structure and search for similar patterns in the RNAdex database
About Graph-Based Structure Search
This tool uses a graph-based subgraph isomorphism algorithm to search for RNA structural patterns
matching your custom-drawn motif. Unlike type-based searches that use pre-defined motif types, this search allows you to:
Define any arbitrary RNA structural pattern
Include non-Watson-Crick (non-WC) interactions such as wobble pairs, Hoogsteen pairs, and other non-canonical base pairs
Search across RNA structures extracted from the Protein Data Bank (PDB)
Retrieve matching 3D atomic coordinates and graph representations
Note: Complex structures may take several minutes to process (current timeout: 20 minutes).
For very complex patterns, processing time may exceed the timeout limit. The algorithm performs exact subgraph matching with edge attribute constraints.
How to Use:
Add Node: Click on the canvas to add nucleotide nodes (each node represents one nucleotide)
Add Edge: Select edge type first, then click two nodes to connect them with the chosen interaction type
Delete: Click on a node or edge to select it, then press Delete key or click Delete button to remove it
Clear All: Remove all nodes and edges from the canvas to start over
Load Example: Choose a simple pattern or a database-backed bulge or internal-loop query below
Edge Types (Select before adding edges):
Edge Legend:
Covalent (Backbone)
Watson-Crick Base Pair
Non-Watson-Crick Base Pair
Load a query example
Choose a ready-to-edit topology. Search results are topology candidates.
4 nt · 4 edges
6 nt · 7 edges
5 nt · 5 edges
6 nt · 7 edges
8 nt · 10 edges
📖 Quick Guide: How to Build Your Motif
1
Add Nodes (Nucleotides)
Click anywhere on the canvas above
Each click adds a numbered nucleotide
Nodes appear as blue circles with numbers
2
Add Edges (Connections)
Select edge type button (Covalent, Watson-Crick, etc.)
Click first node, then second node
Edge will appear as a colored line
💡 Tip: Load any example above, edit its nodes or edges, and then submit the graph to search for matching topology candidates.