RIME

Tutorial: Using the RIME Web Server

Overview

Welcome to the RIME Web Service. This service allows users to predict RNA-RNA interactions solely from sequence information. Starting from two long RNA sequences, the application calculates RIMEfull prediction scores for 200x200 nucleotides windows with a 100 nucleotides step. This tutorial will guide you through the steps of using the web service, from inputting your data to retrieving your results

Step-by-Step Instructions

Step 1: Accessing the Web Server

• Open your web browser and navigate to the https://tools.tartaglialab.com/rna_rna

Step 2: Inputting Your Data

You can input your data in one of the following ways:

• Text submission:
  • Scroll down to the input window labeled "Text submission".
  • Type or paste your two RNA sequences in the FASTA format.
  

• File submission:
  • Click on the "File submission" button.
  • Select 2 files from your computer. Each file should be a FASTA.
  

Step 3:Submitting Your Data

• Submit:
  • Click the "Submit" button to start the analysis process.
  • You will be redirected to a page that confirms your submission and provides a tracking ID (web link).

Step 4: Retrieving Your Results

• Notification:
  • If you provided an email address, you will receive an email with a link to your results once the analysis is complete
• Download Results:
  • Click on the provided link to access your results.
  • Table View: Navigate to the Table tab to view a detailed table displaying RIMEfull prediction scores across all 200x200 nucleotide windows. The same table can be downloaded in BEDPE format by clicking on the “Get table” button.
  • Plot View: Switch to the Plot tab to visualize the same data as a heatmap for an intuitive representation of the results.

Table Description

This table represents pairwise RNA fragment interactions, where each row corresponds to a pairwise combination between two RNA sequence fragments and their interaction score. The coordinate system is zero-based, half-open, meaning that the coordinate of the first nucleotide of the sequence is 0 and that the end coordinate is 1 + the actual end position.

Columns:

window_id1: Identifier for the first RNA sequence.

start1, end1: Start and end coordinates of the window in the first RNA sequence.

window_id2: Identifier for the second RNA sequence.

start2, end2: Start and end coordinates of the window in the second RNA sequence.

RIME_score: Interaction score between the two RNA fragments, ranging from 0 to 1. Values greater than 0.5 indicate a positive interaction propensity.

strand1, strand2: Strand orientation of the RNA sequences (always set to +).

Plot Description: RNA Interaction Heatmap

This plot is a heatmap representation of the contact matrix between two RNA sequences, where each cell corresponds to an interaction score between a specific fragment of the first RNA and a specific fragment of the second RNA.

Axes:

X-axis: Positions in the first RNA sequence (window_id1) defined by start1, end1.

Y-axis: Positions in the second RNA sequence (window_id2) defined by start2, end2.

Heatmap Representation:

Each cell in the matrix represents the RIME_score, which quantifies the interaction propensity between the two RNA fragments.

The color intensity of the cell corresponds to the interaction score.

The numerical RIME_score is displayed within each cell to provide an exact interaction value.

This visualization helps identify regions of strong interaction between the two RNA sequences, facilitating the study of potential RNA-RNA binding sites and functional interactions.

Additional Information

• Analysis Time:
• RIME typically completes within a few minutes for most pairs.
• Troubleshooting:
• File Upload Issues:
• Ensure your files are in the correct FASTA format. Both T and U characters are allowed to represent uracil nucleotides.
• No Results Email:
• Check your spam/junk folder if you do not receive an email within the expected timeframe.
• Ensure you entered the correct email address.