RNA secondary structure prediction based on machine learning

KNetFold is a software for predicting the consensus RNA secondary structure for a given alignment of nucleotide sequences. You can read about the scientific background of this software in the help document or in our recent publication.

The CyloFold web server is an option for analyzing single RNA sequences. For analyzing alignments of RNA sequences you also might want to try our 3D sequence logo generator called CorreLogo .

Quick start

For a really quick start, simply use this form filled with the example tRNA alignment and click "submit". This example alignment is based on the tRNA entry of the RFAM database. If you want to compute a prediction using your own set of sequences, you need to paste a set aligned RNA sequences (in FASTA format) into the sequence text area of the empty submission form. Providing the email address is optional. Be aware that computing the results can take more than an hour (depending on the length of the submitted alignment). The use of the options is explained in the help text. To obtain old results go to the result retriever page.

Fill text area with example sequences:


Bindewald, E and Shapiro B.A (2006): RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA. 12(3): 342-352 (2006).