This tool identify FISH probes from 16S sequences. Given a clade, it identifies sequences (of a given length) that belong to that and only that clade.
The mOTU profiler requires:
- Python 3 (or higher)
First clone the repo:
git clone https://github.com/AlessioMilanese/FISH_probes.git
Setup:
cd FISH_probes
python setup.py bdist_wheel
pip install --no-deps --force-reinstall dist/*.whl
You will need a fasta file with 16S sequences and relative taxonomy.
Test the design pipeline:
fish_probes design -s test/seq.fa -t test/tax -c Firmicutes -k 7
It will use the sequences in test/seq.fa (taxonomy in test/tax) to identify probes of length 7 that are unique for Firmicutes.
Find the properties of a specific probe:
fish_probes test_probe -i "AATGCATCGATC"
It will identify GC content, sequence entropy and melting temperature of the probe AATGCATCGATC.