Skip to main content

Finds target sites for the miRNAs in genomic sequences.

Project description

metaRNA finds potential target sites for the microRNAs in genomic sequences. It is built on miRanda, an algorithm for detection and ranking of the targets of microRNA.

Build Status
PyPi Status
Python Versions
License

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)

Installation

metaRNA supports Python versions 2.7, 3.3, 3.4, and 3.5. It requires the Vienna RNA package which must be installed before installing metaRNA.

After Intalling Vienna RNA package, metaRNA may be installed simply by executing:

$ pip install metarna

metaRNA is currently tested on Mac OSX and Ubuntu, however other Unix based systems should be supported. It isn’t tested on Windows yet.

Description

The miRanda algorithm works in two phases. In phase one, the potential target sites are reported based on query microRNA and reference (CDNA) sequence. These targets are scored and the high scoring alignments are then used in second phase, where the folding routines of RNAlib library are utilised to calculate the minimum free energy of the resulting combinations.

Further Information

Citing in publications

Please cite the original miRanda library, and Vienna RNA library. The citations can be obtained from the links above.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

metarna-4.0.0.tar.gz (10.5 kB view hashes)

Uploaded Source

Built Distributions

metarna-4.0.0-py3.5-macosx-10.11-x86_64.egg (103.0 kB view hashes)

Uploaded Source

metarna-4.0.0-cp35-cp35m-macosx_10_11_x86_64.whl (101.6 kB view hashes)

Uploaded CPython 3.5m macOS 10.11+ x86-64

metarna-4.0.0-cp27-none-macosx_10_11_x86_64.whl (101.4 kB view hashes)

Uploaded CPython 2.7 macOS 10.11+ x86-64

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page