metaRNA, find target sites for the miRNAs

metaRNA finds potential target sites for the microRNAs in genomic sequences.

  • Written in Python
  • Built on miRanda.

It is built on miRanda, an algorithm for detection and ranking of the targets of microRNA.

Quickstart

from metarna.target_scan import scan, free_energy

gene_sequence = (
    "ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCC"
    "CCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGC"
    "CTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGG"
)

mirna_sequence = "UGGCGAUUUUGGAACUCAAUGGCA"

# Get free Energy value:
delta_g = free_energy(gene_sequence, mirna_sequence)

# Get full targets information:
targets = scan(gene_sequence, mirna_sequence)

# Specifying Calculation Parameters
targets = scan(gene_sequence, mirna_sequence, scale=5.0)

Contents

Indices and tables