This tutorial explains how to use the miRQuest tool to perform benchmarking and identification of microRNAs (miRNAs). It describes accessing the tool interface and selecting prediction tools, parameters, and file inputs for either benchmarking known miRNA sequences or identifying miRNAs in a user's dataset. Benchmarking requires positive and negative sequence files while identification only needs a multi-FASTA file. Process triggers the analysis and results are emailed.

1. Tutorial - How to use
miRQuest

2. Trough this short tutorial you’ll learn how to:
 Perform benchmark between the trending miRNA prediction tools
 Identify miRNA using those tools with your own datasets

3. The first step is to go to the TOOL tab, marked with the yellow arrow.

4.  Once there, you should see the currently available tools for ncRNA research.

5.  After you choose one or more of them, you’ll be able to set (if needed) different parameters. Default
values are shown.

6.  Leaving the mouse over the information icon will provide useful information related to the
parameter

7.  Once done with the software parameters, you’ll be ask to choose between the two main
functionalities of miRQuest: Benchmark or Identification

8. ● For instance, in the case you choose to perform a Benchmark analysis, you need to provide an e-mail
to receive the results when ready, and another 2 files:

9. Positive file: Multi FASTA file containing proved miRNA sequences. It must have FASTA, FA or TXT
extension and it cannot be larger than 5 mb. For example:
Negative file: Multi FASTA file containing non miRNA sequences (i.e. mRNA sequences). It must have
FASTA, FA or TXT extension and it cannot be larger than 5 mb. For example:

10. ● In the case you want just try the performance of the software, we also provide some exemplary
files, also availables in the Downloads section of the webpage:

11. On the other hand, if you choose to perform a Identification analysis, you only need to point out your e-
mail and the multi FASTA file where to make the predictions.

12.  Finally, clicking Process will trigger the calculation. You should receive an email with the graphs &
statistics among the different selected softwares.

14. Tutorial - How to use
miRQuest
mirquest.integrativebioinformatics.me