Running script to generate unique motifs from miRBase - Gu-Lab-RBL-NCI/QuagmiR GitHub Wiki

Generates unique motifs for miRNA of all species while taking into account indistinguishable miRNA (dupli-miRNA) and paralogs

Dependencies

  1. Download miRNA.xls.gz or miRNA.xls.zip from miRBase and unzip file
  2. Locate script: /Motifs/reports/getUniqueMirbaseMotif.R

Setup

  1. Change base_path variable to directory where downloaded miRBase file is located (e.g. '/Users/doejohn/Documents/motifs/')
  2. Change motif_len variable to desired motif length
  3. Change include_pos variable to T to include motif position in fasta file and F to exclude
  4. Change motif_start variable to where the motif should be created from the sequence
  5. Run script

Output

  • motif_list_species_mirbase_22.fa records all found unique motifs in fasta format
  • species-miRBase22.tsv records indistinguishable miRNA (dupli-miRNA), paralogs, all generated miRNA IDs, motifs, and miRBase data
  • motif_coverage.tsv records the percent of miRNA for which a unique motif was found

Compiled motif list

  • A list unique miRNA motifs for organisms reported in miRBase22 can be found here.