DNA Sequence Translator

Inputted DNA sequence filters through organism genomes from Genbank files for matching sequence in a protein. Once the sequence matches a portion of the corresponding protein CDS (coding sequence) region, the function will return the organism and location the sequence was found at in the protein.

Organism genomes were obtained using GenBank files from NCBI,
i.e. complete genome for Paramecium bursaria Chlorella virus

Submitting 'CGCAGGCGCT' will return
in protein 'YP_004678872.1'
in organism 'NC_000852.5'
at location '1370..1380'

Celery asynchronous architecture

Resources

Utilized BioPython library and SeqIO to parse genbank files that store sequence data, representing nucleotide sequences.
Asynchronous search capabilities with celery and Redis as message broker and result store.
React frontend uses local storage to persist searched sequences and generated results.

To run locally

Have instance of React app, server, and celery worker running

To run React app

cd ./frontend
npm start

To run celery worker

cd ./backend
pipenv shell
celery -A sequences_api worker -l info

To run Django server

cd ./backend
pipenv shell
pip install -r requirements.txt
python manage.py runserver

To run tests

cd ./frontend
npm run test

Available on

UI http://localhost:3000/
and
API http://localhost:8000/api/:DNASequence
to get results from Celery TaskResult table
http://localhost:8000/api/results/tasks