3. Quick Start

3.1. Input files

The most important input file is a DNA sequence. This could be a multifasta sequence that belongs from a common specie (i.e. complete genome or group of particular sequences). At the same time, previous to execute miRNAture a you have to download a pre-calculated dataset (as indicated on Pre-calculated datasets Section) that contains default data as CMs, HMMs, and required files to perform mature prediction. Once located in your computer, the path might be indicated with the flag -dataF.

3.1.1. Activate the mirnature environment

conda activate mirnature

3.1.2. Run miRNAture

A complete mode should be run as follows:

./miRNAture -stage complete -dataF <Precalculated_folder> \
            -speG <Target Genome> -speN <Specie_name> \
            -speT <Tag_specie> -w <Output_dir> \
            -m <Mode> (-str <Blast_strategy>) \
            -blastq <Blast_queries_folder>

But it is always recommended to look up specific parameters. Do not use the default parameters for all experiments.

3.1.3. Output files

Final predicted miRNAs will be written on the <Output_dir> indicated with the -w flag. The final candidates are described on the folder Final_miRNA_evaluation/ as follows:

Final_miRNA_evaluation/
├── Fasta/
├── MFE/
├── miRNA_annotation_<Tag_specie>_accepted_conf.bed
├── miRNA_annotation_<Tag_specie>_accepted_conf.gff3
├── miRNAture_summary_<Tag_specie>.txt
└── Tables/

Inside this folder, miRNAture will create 3 folders containing their correspondent results: sequences in fasta format (Fasta/), minimum free energy and lengths from described sequences (MFE/) and the supporting information ordered in tables for each annotated candidate (Tables/). Additionally, associated genomic positions for the miRNA candidates are reported in BED and GFF3 formats and a summary file, miRNAture_summary_<Tag_specie>.txt, that describes overall descriptive statistics from found miRNA families.

3.1.4. Pre-calculated datasets

Pre-calculated data composed by miRNA CMs, HMMs and required input files to perform mature annotation has to be downloaded before run the full miRNAture pipeline. Available datasets are listed below:

• NEW: Curated metazoan families from miRBase v.22.1, available to the structural validation stage.

• Required data to re-annotate human miRNAs: include CMs and HMMs build from miRBase without human sequences. Stored in Zenodo here.