Alignment API

Local and Global Alignment in python

About The Project

The objective of this sequence alignment technique is to place a query sequence end-to-end with the known sequence so as to find out some relationship like structural, functional, or evolutionary between them.
I implemented in this project local and global in python then deliver as API using django rest freamework

Built With

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Getting Started

Prerequisites

• Python <= 3.10.6
• Pip <= 22.0.2
• Python virtual environment

1. Clone the repo

   git clone https://github.com/mohmmedfathi/Alignment-Api && cd Alignment-Api

2. Create virtual environment

   python3 -m venv venv

3. Activate virtual environment

   source venv/bin/activate

4. Install requirements

   pip install -r requirements.txt

5. Migrate models

   python manage.py migrate

6. Run server

   python manage.py runserver 

Usage

We have two endpoint :

Global endpoint

http://127.0.0.1:8000/api/alignment/global/

you have to enter 5 value :

• first sequence is seq1
  

• second sequence is seq2
  

• gap is gap
  

• match is match
  

• mismatch is mismatch
  

sample input :

{ 
"seq1":"aaac",
"seq2":"agc", 
"gap" : -2,
"match":1, 
"mismatch" : -1 
}

output for previous input :

HTTP 201 Created
Allow: OPTIONS, GET, POST

{
    "id": 1,
    "seq1": "aaac",
    "seq2": "agc",
    "aligned1": "aaac",
    "aligned2": "ag-c",
    "score_matrix": "[0, -2, -4, -6],[-2, 1, -1, -3],[-4, -1, 0, -2],[-6, -3, -2, -1],[-8, -5, -4, -1]",
    "traceback_matrix": "['done', 'left', 'left', 'left'],['up', 'diag', 'left', 'left'],['up', 'up', 'diag', 'left'],['up', 'up', 'up', 'diag'],['up', 'up', 'up', 'diag']"
}

Local endpoint

http://127.0.0.1:8000/api/alignment/local/

you have to enter 5 value :

• first sequence is seq1
  

• second sequence is seq2
  

• gap is gap
  

• match is match
  

• mismatch is mismatch
  

sample input :

{
"seq1": "ATGCT",
"seq2": "AGCT",
"gap": -2,
"match": 1,
"mismatch":-1
}

output for previous input :

HTTP 201 Created
Allow: POST, GET, OPTIONS

{
    "id": 1,
    "seq1": "ATGCT",
    "seq2": "AGCT",
    "score_matrix": "[0, 0, 0, 0, 0, 0],[0, 1, 0, 0, 0, 0],[0, 0, 0, 1, 0, 0],[0, 0, 0, 0, 2, 0],[0, 0, 1, 0, 0, 3]",
    "best_score": 3,
    "alignment1": "ATGCT",
    "alignment2": "A-GCT"
}

• you can see the models in Admin Panel

  

To create a superuser

python manage.py createsuperuser

Contact

Mohammed Fathi - mohmmedfathi.123@gmail.com

Project Link: https://github.com/mohmmedfathi/Alignment-Api/