SPOT-RNA: RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.

Our resources are limited. If you wish to run several batches per day please make use of the downloadable package or contact the administrator directly.


E-mail address (optional):
Target (optional):
Input your RNA Sequences: Maximum: 2000 nts, Only one RNA sequence at a time


To run SPOT-RNA for long sequences or batch of sequences, please use standalone version of SPOT-RNA mentioned below.

Standalone Program to Run Locally:



bpRNA: Initial Learning (Training TR0, validation VL0, and test TS0) Dropbox or Nihao Cloud

PDB: Transfer Learning (Training TR1, validation VL1, and test TS1) Dropbox or Nihao Cloud


Singh, J., Hanson, J., Paliwal, K., Zhou, Y. RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning. Nat Commun 10, 5407 (2019)