RNAcomp2D is a web application for RNA secondary structure prediction and comparison using multiple methods. You can try it out at the web server. For more information, check out and cite our paper: "RNAcomp2D: a visual tool to compare multiple predictions of RNA secondary structure," Rosario Vitale, Diego H. Milone, Georgina Stegmayer, (under review) 2025.
RNAcomp2D allows you to upload a sequence or search it on RNAcentral. If secondary structure is available on RNAcentral, it will be shown in the results page.
You can also upload a FASTA file with multiple structures for comparison. If description contains the word "reference", it will be shown in the results page as a reference structure. Else, it will be shown as another method prediction. Some examples of FASTA files are available here.
Then, you can select one or more methods to predict the secondary structure, compare the predictions, and download the results. At the moment, the following methods are available:
- RNAfold (paper)
- RNAstructure (paper)
- LinearFold (paper)
- LinearPartition (paper)
- sincFold (paper)
- UFold (paper)
- REDfold (paper)
If reference structure is available, it will be shown in the results page with the predicted structures of the selected methods.
This repository contains the source code for the web application and instructions to deploy it on your own server.
To install and run the web application, you need to have Git, Docker and Docker Compose installed. Follow the instructions in the official documentation to install them and make sure you have Docker daemon running. After that, you can go to the next step.
First, clone the repository and navigate to the root directory:
git clone https://github.com/sinc-lab/RNAcomp2D.git
cd RNAcomp2D
Then, run the following command to build and run the web application:
docker-compose -f docker-compose-no-proxy.yml up -d
This may take a few minutes. Once it is done, you can access the web application at http://localhost:8000.
If you have any questions or need help, please send an email to rvitale@sinc.unl.edu.ar.