DNA Probe Generation

This repository contains a simple python executable script that allows analyzing a given protein sequence to extract the most suitable low variability region which could possibly be converted into its cDNA oligonucleotides to provide the highest hybridization binding affinity and thus better accuracy.

How to use

• After cloning the current repository or downloading a zipped archive of it, enter into the local downloaded repository directory cd <Repository Directory>

• convert the current script into an executable script using chmod a+x probing.py

• move or copy the executable script into your /usr/bin to be OS wide Available, mv ./probing.py /usr/bin/probing

• Afterwards, when you have your gene protein product, and you want to generate a cDNA oligonucleotides probe to specifically bind to your gene of interest in a cloning experiment, Please follow the following steps.

probing --help

usage: probing [-h] [-f FASTA] [-s SIZE] [-t TOP]

optional arguments:
  -h, --help            show this help message and exit
  -f FASTA, --fasta FASTA
                        Protein Fasta File
  -s SIZE, --size SIZE  required probe size/length in bases
  -t TOP, --top TOP     Return Top (N) of probes having the lowest variation
                        in sequence

Example

Extracting the best probe to use for performing hybridization probing to SARS-COV 2 Protease Gene would be like the following:

• sars2.protease.fa file is SARS-COV 2 protease protein sequence in fasta file, we are going to use it to generate the best top 3 probes to use for phishing recombinant colonies that contain that particular protease gene

probing --fasta ./sars2.protease.fa --size 12 --top 3

        AA Sequence : MHHM
        DNA Sequence : ATGCATCATATG
        Hybridization Affinity : 83.33%
        Variable bases # : 2
        

        AA Sequence : KMAF
        DNA Sequence : AAGATGGCTTTT
        Hybridization Affinity : 75.00%
        Variable bases # : 3
        

        AA Sequence : MAFP
        DNA Sequence : ATGGCTTTTCCT
        Hybridization Affinity : 75.00%
        Variable bases # : 3

Thank you.