IIT_Roorkee_Web_Application

iGEM Indian Institute of Technology Roorkee 2020 - TailScout Web_Application

Basic Instructions for running the codes individually on your systems :

Dependencies:

- Python, To install python on your system

• sudo apt install python3.7

- Python dependency xmltramp2

• pip install --upgrade pip xmltramp2 requests

- Perl, To install perl on your system

• sudo apt-get update
• sudo apt-get install perl

For Checking the gene_detection.py code, which basically has two main fnuctions: 1. search_the_db_for_tails(input_bacteria) 2. find_amino_seq(gene_code)

- Run the python script with arguments such as search_the_db_for_tails('staphylococcus aureus') or find_amino_seq('YP_009006775.1')

Can use any of the bacteria from ESKAPE or any gene_code from the phage_details.csv file

For running Clustal omega MSA API python code:

- In order to run the MSA, input sequence fasta file and clustalo.py script should be in the same directory.
- Next, after running the script, the result files are stored in the same direcotry.
- Last,to run the script following example should be used on terminal or cmd:

python clustalo.py --email your@email.com --sequence <sequence_file_name.fasta>

For running the jpred api on your system using command prompt:

- Next, go to the directory which has jpredapi file and the seq file as well
- Then type 'perl jpredapi submit file=filename mode=batch format=fasta email=emailid@domain.com name=my_test_job skipPDB=on'
on the command prompt.

Here, 'name' and 'skipPDB' parameters are optional but you need to provide other parameters, you will recieve the result on the mentioned email id

• For creating the database files such as phage_setails.csv and sequence_phages.faa we used NCBI(National Center for Biotechnology Information) and Genomenet virushostdb databases.
• If you also want to make your own set of database files you can take them from these or similar databases.