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)
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