AlessioMilanese / FISH_probes

Scripts to design FISH probes for 16S sequences

16S FISH probes

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.

Pre-requisites

The mOTU profiler requires:

• Python 3 (or higher)

Installation

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.

Simple examples

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.