RNA Matrix


This RNA Matrix Program converts an RNA secondary structure into a matrix representation of the RNA's graph. Specifically, it takes a ".ct" or ".Bpseq" file format and determines the number of vertices within the RNA structure, the Laplacian matrix, the eigenvalues, and the order of the labeled graph. To learn more about the concepts that are involved with this program, please visit the Program Description.


Upload File:   

File Type:


Graph Representation: Tree Graph Dual Graph (default)

Enter Email: (Required for batch processing - See below)




  1. For ".ct", ".bpseq", and ".gzip" files, please make sure the file extension is not ".txt". File extension should match the file format
  2. If you upload an adjacency matrix, please verify that the file is in plain text with the extension ".txt"
  3. The Max file size allowed is 20MB
  4. For Unix/Linux/Mac users, you can verify that your ".ct" files are properly formated using "vi". Windows users may use "notepad" to make sure the file is in plain text


Batch Processing:

Users can also upload a group of ".ct" files for batch processing. To prepare files, please do the following on your local machine:

  1. Save your ".ct" files into one directory (for example: my_ct_dir)
  2. Tar your direcory using a command similar to the following on Unix: "tar cvf ./my_files.tar ./my_ct_dir"
  3. Compress your tar: "gzip my_files.tar"
  4. Upload your compressed file above and provide email address for results

For sample files, please save the following to your computer and upload using the form:

Sample .ct file: tRNA (NDB:TRNA12)

Sample dot-bracket notation file

Sample Adjacency Matrix for Dual Graphs

Sample Adjacency Matrix for Tree Graphs


Page | by Dr. Radut